Despite the widespread use of chemotherapeutic agents, their reliance on apoptosis often limits therapeutic efficacy and leads to drug resistance. To overcome these challenges, alternative cell death Show more
Despite the widespread use of chemotherapeutic agents, their reliance on apoptosis often limits therapeutic efficacy and leads to drug resistance. To overcome these challenges, alternative cell death mechanisms such as cuproptosis have gained significant attention. While previous studies have primarily focused on incorporation of Cu into nanostructures, this work presents the first example of a molecular tripodal Cu(II) complex as a potent cuproptosis inducer. Herein, a series of tripodal Cu(II) complexes were chemically synthesized and biologically evaluated. The most promising compound demonstrated remarkable cytotoxicity in the low micromolar to nanomolar range. Mechanistic studies revealed that the compound catalytically produced hydroxyl radicals in the mitochondria of cancerous cells, causing protein oligomerization and the disruption of iron-sulfur cluster proteins, ultimately triggering cell death by cuproptosis. Contrary to traditional chemotherapeutic agents that cause reduction in tumor size, this compound induced the fragmentation of three-dimensional tumor spheroids. Show less
Abstract The development of multifunctional carriers for gene delivery is a critical challenge in modern therapeutics, particularly in the context of multi‐drug therapy (MDT). In this study, we report Show more
Abstract The development of multifunctional carriers for gene delivery is a critical challenge in modern therapeutics, particularly in the context of multi‐drug therapy (MDT). In this study, we report the synthesis and characterization of fluorinated guanidino‐polyamine conjugates based on low‐generation polyamidoamine (PAMAM) dendrimers and low molecular weight polyethyleneimine (PEI) polymers. These conjugates are designed to act as both efficient transfection agents and artificial ribonucleases, providing a dual‐function approach to gene therapy. The functionalization with fluorinated guanidino groups enhances DNA condensation, facilitates intracellular delivery, and enables tracking via 19 F MRI. Potentiometric and kinetic studies demonstrate their phosphodiesterase activity on a model compound, with PAMAM G4 derivatives exhibiting the highest catalytic efficiency. Biolayer interferometry and transfection experiments confirm mRNA cleavage activity, leading to reduced gene expression. Additionally, transfection studies with plasmid DNA (pDNA) indicate high gene delivery efficiency, surpassing conventional PEI‐based systems while maintaining low cytotoxicity. These findings suggest that the conjugates presented herein, and in particular those derived from low‐generation PAMAM dendrimers, can serve as promising multifunctional carriers for a combined diagnostic and MDT, offering a new strategy for synergistic gene delivery and RNA degradation. Show less
Dean G. Brown · 2025 · Journal of Medicinal Chemistry · ACS Publications · added 2026-04-20
An analysis of dose, dose frequency, human pharmacokinetics, and potential drug-drug interactions (DDI) was performed on small-molecule oral drugs approved by the FDA from 2020 to 2024 (n = 104 Show more
An analysis of dose, dose frequency, human pharmacokinetics, and potential drug-drug interactions (DDI) was performed on small-molecule oral drugs approved by the FDA from 2020 to 2024 (n = 104). Although most oral drugs are administered QD (67%), BID and TID regimens are also regularly approved (32%). First-in-class (FIC) drugs and drugs with Orphan Drug Designation (ODD) have a higher frequency of BID or TID administration compared to drugs without those designations (BID and TID = 50% for FIC drugs vs 19% for non-FIC; BID and TID = 41% for ODD vs 20% non-ODD). Most drugs are >95% plasma protein bound (58%), with a large fraction >99% bound (29%). Of these drugs, 22% have black box warnings and 42% list contraindications. An examination of DDI revealed the most frequent warning around CYP3A4 induction (60%). These findings will help medicinal chemists better understand and predict typical and nontypical profiles of oral drugs. Show less
Introduction 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 i Show more
Introduction 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.
Methods Bibliometric analysis was performed by extracting data linking mitochondria to cancer pathogenesis over the
period 1990–2023 from the PubMed database which has a precise and specific search engine. Only articles and reviews
were considered. Since PubMed does not support analyses by countries or institutions, we utilized InCites, an analytical
tool developed and marketed by Clarivate Analytics. We also used the VOSviewer software developed by the Centre for
Science and Technology Studies (Bibliometric Department of Leiden University, Leiden, Netherlands), which enables
us to graphically represent links between countries, authors or keywords in cluster form. Finally, we used iCite, a tool
developed by the NIH (USA) to access a dashboard of bibliometrics for papers associated with a portfolio. This module
can therefore be used to measure whether the research carried out is still basic, translational or clinical.
Results In total, 169,555 publications were identified in PubMed relating to ‘mitochondria’, of which 34,949 (20.61%)
concerned ‘mitochondria’ and ‘dysfunction’ and 22,406 (13.21%) regarded ‘mitochondria’ and ‘cancer’. Hence, not all mitochondrial dysfunctions may lead to cancer or enhance its progression. Qualitatively, the disciplines of journals were
classified into 166 categories among which cancer specialty accounts for only 4.7% of publications. Quantitatively, our
analysis showed that cancer/neoplasms in the liver (2569 articles) were placed in the first position. USA occupied the
first position among countries contributing the highest number of publications (5695 articles), whereas Egypt came in
the thirty-eight position with 84 publications (0.46%). Importantly, USA is the first-ranked country having both the top
1% and 10% impact indicators with 207 and 1459 articles, respectively. By crossing the query ‘liver neoplasms’ (155,678)
with the query ‘mitochondria’ (169,555), we identified 1336 articles in PubMed over the study period. Among these
publications, research areas were classified into 65 categories with the highest percentage of documents included in
biochemistry and molecular biology (28.92%), followed by oncology (23.31%).
Conclusions This study underscores the crucial yet underrepresented role of mitochondria in cancer research. Despite
their significance in cancer pathogenesis, the proportion of related publications remains relatively low. Our findings
Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s12672-025-
02139-5.
* Abeer El Wakil, abeer_elwakil@alexu.edu.eg; Patrick Devos, patrick.devos@univ-lille.fr; Heba Abdelmegeed, hn.abdelmegeed@
nrc.sci.eg; Alaa Kamel, alaa.kamel_pg@alexu.edu.eg | 1Department of Biological and Geological Sciences, Faculty of Education, Alexandria
University, Alexandria 21526, Egypt. 2Université Lille, Lillometrics, 59000 Lille, France. 3CHU Lille, Direction de la Recherche et de
l’Innovation, 59000 Lille, France. 4Department of Chemistry of Natural Compounds, National Research Centre, Giza, Egypt. 5Department
of Zoology, Faulty of Science, Alexandria University, Alexandria, Egypt.
Discover Oncology
(2025) 16:517
| https://doi.org/10.1007/s12672-025-02139-5
Vol.:(0123456789)
Research
Discover Oncology
(2025) 16:517
| https://doi.org/10.1007/s12672-025-02139-5
highlight the need for further research to deepen our understanding of mitochondrial mechanisms in cancer, which
could pave the way for new therapeutic strategies.
Graphical Abstract Show less
Charles H. Reynolds · 2025 · ACS Medicinal Chemistry Letters · ACS Publications · added 2026-04-20
Drug discovery has seen dramatic change over the last 25 years. The vertically integrated large company model prevalent for more than 50 years has at least partly been replaced with a more distributed Show more
Drug discovery has seen dramatic change over the last 25 years. The vertically integrated large company model prevalent for more than 50 years has at least partly been replaced with a more distributed drug discovery enterprise that includes large numbers of small research organizations. Show less
2025 · International journal of molecular sciences · MDPI · added 2026-04-21
Academic Editor: Sabrina Venditti Received: 22 May 2025 Revised: 5 July 2025 N6-methyladenosine (m6A) represents the most common and thoroughly investigated RNA modification and exerts essential funct Show more
Academic Editor: Sabrina Venditti Received: 22 May 2025 Revised: 5 July 2025 N6-methyladenosine (m6A) represents the most common and thoroughly investigated RNA modification and exerts essential functions in regulating gene expression through influencing the RNA stability, the translation efficiency, alternative splicing, and nuclear export processes. The rapid development of high-throughput sequencing approaches, including miCLIP and MeRIP-seq, has profoundly transformed epitranscriptomics research. Show less
2025 · · Cold Spring Harbor Laboratory · added 2026-04-20
Abstract
Transcription of ribosomal RNA (rRNA) by RNA Polymerase I (Pol I) is often upregulated in cancer to facilitate rapid cell growth and proliferation, and has emerged as a potent Show more
Abstract
Transcription of ribosomal RNA (rRNA) by RNA Polymerase I (Pol I) is often upregulated in cancer to facilitate rapid cell growth and proliferation, and has emerged as a potential target for chemotherapeutic agents. BMH-21 and Pt(II) chemotherapeutic agent oxaliplatin are well documented as inhibitors of Pol I activity, however the underlying mechanisms for this inhibition are not completely understood. Here, we applied chromatin immunoprecipitation sequencing (ChIP-seq) techniques and immunofluorescence imaging to probe the influence of oxaliplatin and BMH-21 on Pol I machinery. We demonstrate oxaliplatin and BMH-21 induce early nucleolar stress leading to the formation of “nucleolar caps” containing Pol I and upstream binding factor (UBF) which corresponds with broad reductions in ribosomal DNA (rDNA) occupancy of Pol I. Distinct occupancy patterns for the two compounds are revealed in ChIP-seq experiments. Taken together, our findings suggest that in vivo, oxaliplatin does not induce Pol I inhibition via interrupting a specific step in Pol I transcription, while treatment with BMH-21 induced unique polymerase stalling at the promoter and terminator regions of the human ribosomal RNA gene. Show less
Redox, a native modality in biology involving the flow of electrons, energy, and information, is used for energy-harvesting, biosynthesis, immune-defense, and signaling. Because electrons (in contrast Show more
Redox, a native modality in biology involving the flow of electrons, energy, and information, is used for energy-harvesting, biosynthesis, immune-defense, and signaling. Because electrons (in contrast to protons) are not soluble in the medium, electron-flow through the redox modality occurs through redox reactions that are sometimes organized into pathways and networks (e.g., redox interactomes). Redox is also accessible to electrochemistry, which enables electrodes to receive and transmit electrons to exchange energy and information with biology. In this Perspective, efforts to develop electrochemistry as a tool for redox-based bio-information processing: to interconvert redox-based molecular attributes into interpretable electronic signals, are described. Using a series of Case Studies, how the information-content of the measurements can be enriched using: diffusible mediators; tuned electrical input sequences; and cross-modal measurements (e.g., electrical plus spectral), is shown. Also, theory-guided feature engineering approaches to compress the information in the electronic signals into quantitative metrics (i.e., features) that can serve as correlating variables for pattern recognition by data-driven analysis are described. Finally, how redox provides a modality for electrogenetic actuation is illustrated. It is suggested that electrochemistry's capabilities to provide real-time, low-cost, and high-content data in an electronic format allow the feedback-control needed for autonomous learning and deployable sensing/actuation. Show less
AbstractPhotoactivatable metal complexes offer the prospect of novel drugs with low side effects and new mechanisms of action to combat resistance to current therapy. We highlight recent progress in t Show more
AbstractPhotoactivatable metal complexes offer the prospect of novel drugs with low side effects and new mechanisms of action to combat resistance to current therapy. We highlight recent progress in the design of platinum, ruthenium, iridium, gold and other transition metal complexes, especially for applications as anticancer and anti‐infective agents. In particular, understanding excited state chemistry related to identification of the bioactive species (excited state metallomics/pharmacophores) is important. Photoactivatable metallodrugs are classified here as photocatalysts, photorelease agents and ligand‐activated agents. Their activation wavelengths, cellular mechanisms of action, experimental and theoretical metallomics of excited states and photoproducts are discussed to explore new strategies for the design and investigation of photoactivatable metallodrugs. These photoactivatable metallodrugs have potential in clinical applications of Photodynamic Therapy (PDT), Photoactivated Chemotherapy (PACT) and Photothermal Therapy (PTT). Show less
2025 · Dalton Transactions · Royal Society of Chemistry · added 2026-04-20
High-Grade Serous Ovarian Cancer (HGSOC) is the most common and lethal subtype of ovarian cancer, known for its high aggressiveness and extensive genomic alterations. Typically diagnosed at an advance Show more
High-Grade Serous Ovarian Cancer (HGSOC) is the most common and lethal subtype of ovarian cancer, known for its high aggressiveness and extensive genomic alterations. Typically diagnosed at an advanced stage, HGSOC presents formidable challenges in drug therapy. The limited efficacy of standard treatments, development of chemoresistance, scarcity of targeted therapies, and significant tumor heterogeneity render this disease incurable with current treatment options, highlighting the urgent need for novel therapeutic approaches to improve patient outcomes. In this study we report a straightforward and stereoselective synthetic route to novel Pd(II)-vinyl and -butadienyl complexes bearing a wide range of monodentate and bidentate ligands. Most of the synthesized complexes exhibited good to excellent in vitro anticancer activity against ovarian cancer cells. Particularly promising is the water-soluble complex bearing two PTA (1,3,5-triaza-7-phosphaadamantane) ligands and the Pd(II)-butadienyl fragment. This compound combines excellent cytotoxicity towards cancer cells with substantial inactivity towards non-cancerous ones. This derivative was selected for further studies on ex vivo tumor organoids and in vivo mouse models, which demonstrate its remarkable efficacy with surprisingly low collateral toxicity even at high dosages. Moreover, this class of compounds appears to operate through a ferroptotic mechanism, thus representing the first such example for an organopalladium compound. Show less
The AI research community plays a vital role in shaping the scientific, engineering, and societal goals of AI research. In this position paper, we argue that focusing on the highly contested topic of Show more
The AI research community plays a vital role in shaping the scientific, engineering, and societal goals of AI research. In this position paper, we argue that focusing on the highly contested topic of `artificial general intelligence' (`AGI') undermines our ability to choose effective goals. We identify six key traps -- obstacles to productive goal setting -- that are aggravated by AGI discourse: Illusion of Consensus, Supercharging Bad Science, Presuming Value-Neutrality, Goal Lottery, Generality Debt, and Normalized Exclusion. To avoid these traps, we argue that the AI research community needs to (1) prioritize specificity in engineering and societal goals, (2) center pluralism about multiple worthwhile approaches to multiple valuable goals, and (3) foster innovation through greater inclusion of disciplines and communities. Therefore, the AI research community needs to stop treating `AGI' as the north-star goal of AI research. Show less
The diversification of ligands provides more opportunities to adjust the photophysical performance as well as the bio-function of Ru(II) complexes as novel photosensitizers. Herein, a kind of Ru(II) c Show more
The diversification of ligands provides more opportunities to adjust the photophysical performance as well as the bio-function of Ru(II) complexes as novel photosensitizers. Herein, a kind of Ru(II) complexes carrying resveratrol derivative, amino-Res, as ligand was designed and synthesized. The representative complex (named Ru4) showed potent anticancer activity under the trigger of 520 nm-light. Lipophilicity and cellular accumulation experiments indicated that Ru4 possessed higher LogPO/W value and cell up-take than Ru1-Ru3 and [Ru(bpy)3]2+. Mechanism study revealed that Ru4 could inhibit cancer cell migration, invasion and cancer stemness. The bio-function of Ru4 was mainly inherited from the amino-Res ligand. The in vivo study demonstrated that Ru4 could inhibit the tumor growth without significant system toxicity. Show less
Tumor metastases account for nearly 90% of cancer-related fatalities. To tackle this issue, chemotherapeutic agents that induce immunogenic cell death (ICD) are being investigated as promising candida Show more
Tumor metastases account for nearly 90% of cancer-related fatalities. To tackle this issue, chemotherapeutic agents that induce immunogenic cell death (ICD) are being investigated as promising candidates for metastatic cancer treatment. Herein, the chemical synthesis and biological evaluation of a novel Ga(III) complex with Schiff bases, [Ga((E)-1-((quinolin-8-ylimino)methyl)naphthalen-2-olato)2][Cl], for potential use in combined chemotherapy and immunotherapy are reported. This compound exhibited broad cytotoxicity against human breast cancer, pancreatic cancer, cervical cancer cell lines, and the noncancerous human fibroblast cell line. Mechanistic investigations revealed that the compound triggers apoptosis and ICD hallmarks, such as translocation of calreticulin, phosphorylation of eIF2α, migration of high mobility group protein 1, and release of adenosine triphosphate. Deeper biological assessment using multicellular tumor spheroids of cervical cancer cell lines, a solid tumor model, demonstrated successful eradication at micromolar concentrations. This study presents one of the few reported Ga(III) complexes capable of inducing immunogenic cell death. Show less
Abstract The first examples of Ru(II) η 6 ‐arene (benzene and p ‐cymene) complexes containing a bidentate triazolylidene‐triazolide ligand have been prepared and fully characterized. Their antiprolife Show more
Abstract The first examples of Ru(II) η 6 ‐arene (benzene and p ‐cymene) complexes containing a bidentate triazolylidene‐triazolide ligand have been prepared and fully characterized. Their antiproliferative effect has been investigated against tumour cells A2780 (ovarian carcinoma), HCT116 (colorectal carcinoma), and HCT116dox (colorectal carcinoma resistant to doxorubicin), and in human dermal fibroblasts. The Ru complex bearing the p ‐cymene arene group exhibited a stronger antiproliferative effect across all tested cell lines, while the benzene‐containing complex displayed higher selectivity toward tumor cells. Both complexes induced apoptosis, likely through ROS production (in the benzene complex), and inhibited tumorigenic processes, including cell migration and angiogenesis. In zebrafish models, they showed strong selectivity for cancer cells with minimal toxicity to healthy cells, effectively reducing the proliferation of HCT116 colorectal cancer cells. This study provides the first in vivo evidence of the anticancer potential of Ru triazolylidenes in zebrafish models. Show less
The emergence of new Mycobacterium tuberculosis (Mtb) strains resistant to the key drugs currently used in the clinic for tuberculosis treatment can substantially reduce the probability of therapy suc Show more
The emergence of new Mycobacterium tuberculosis (Mtb) strains resistant to the key drugs currently used in the clinic for tuberculosis treatment can substantially reduce the probability of therapy success, causing the relevance and importance of studies on the development of novel potent antibacterial agents targeting different vulnerable spots of Mtb. In this study, 28,860 compounds from the library of bioactive molecules were screened to identify novel potential inhibitors of β-ketoacyl-acyl carrier protein synthase I (KasA), one of the key enzymes involved in the biosynthesis of mycolic acids of the Mtb cell wall. In doing so, we used a structure-based virtual screening approach to drug repurposing that included high-throughput docking of the C171Q KasA enzyme with compounds from the library of bioactive molecules including the FDA-approved drugs and investigational drug candidates, assessment of the binding affinity for the docked ligand/C171Q KasA complexes, and molecular dynamics simulations followed by binding free energy calculations. As a result, post-modeling analysis revealed 6 top-ranking compounds exhibiting a strong attachment to the malonyl binding site of the enzyme, as evidenced by the values of binding free energy which are significantly lower than those predicted for the KasA inhibitor TLM5 used in the calculations as a positive control. In light of the data obtained, the identified compounds are suggested to form a good basis for the development of new antitubercular molecules of clinical significance with activity against the KasA enzyme of Mtb.Communicated by Ramaswamy H. Sarma. Show less
A branch of the nucleotide excision repair (NER) pathway, transcription-coupled repair (TCR or TC-NER) specifically operates on the template DNA strand of actively transcribed genes. Initiated by stal Show more
A branch of the nucleotide excision repair (NER) pathway, transcription-coupled repair (TCR or TC-NER) specifically operates on the template DNA strand of actively transcribed genes. Initiated by stalling of elongating RNA polymerase complexes at damaged sites, TC-NER has historically been viewed as "accelerated repair", arguably necessary for the maintenance of vital transcription function. Conversely, the conventional "global genome" (GG-NER) mechanism, operating throughout the genome, is usually regarded as a much slower process, even though it has long been found that differences in repair kinetics between transcribed DNA and the rest of the genome are not manifested for all structural types of DNA damage. Considering that damage detection is the rate-limiting step of overall repair reactions in most cases and that the mechanisms of the initial recognition of modified DNA structure are fundamentally different between TC-NER and GG-NER, it is suggestive to attribute the observed kinetic differences to different damage spectra recognized by the two pathways. This review summarizes current knowledge on the differential requirements of TC-NER and GG-NER towards specific damage types, based on their structural rather than spatial characteristics, and highlights some common features of DNA modifications repaired preferentially or exclusively by TC-NER, while evading other repair mechanisms. Show less
Nucleotide excision repair (NER) is a universal cut-and-paste DNA repair mechanism that corrects bulky DNA lesions such as those caused by UV radiation, environmental mutagens, and some chemotherapy d Show more
Nucleotide excision repair (NER) is a universal cut-and-paste DNA repair mechanism that corrects bulky DNA lesions such as those caused by UV radiation, environmental mutagens, and some chemotherapy drugs. In this review, we focus on the human transcription/DNA repair factor TFIIH, a key player of the NER pathway in eukaryotes. This 10-subunit multiprotein complex notably verifies the presence of a lesion and opens the DNA around the damage via its XPB and XPD subunits, two proteins identified in patients suffering from Xeroderma Pigmentosum syndrome. Isolated as a class II gene transcription factor in the late 1980s, TFIIH is a prototypic molecular machine that plays an essential role in both DNA repair and transcription initiation and harbors a DNA helicase, a DNA translocase, and kinase activity. More recently, TFIIH subunits have been identified as participating in other cellular processes, including chromosome segregation during mitosis, maintenance of mitochondrial DNA integrity, and telomere replication. Show less
A series of cyclometalated platinum-(II) complexes bearing neutral isocyanide or acyclic diaminocarbene ancillary ligands were designed and developed. Their photophysical properties were systematicall Show more
A series of cyclometalated platinum-(II) complexes bearing neutral isocyanide or acyclic diaminocarbene ancillary ligands were designed and developed. Their photophysical properties were systematically studied in different polymer systems: poly-(methyl methacrylate), polystyrene, poly-(isobornyl acrylate), and copolymers based on them. The dependence of luminescent characteristics on the concentration of the doped complex (0.5-10 wt %), composition, and properties of the polymer material was investigated as key factors for the measurement of quantum yields, excited-state lifetimes, and spectral profiles in routine studies. Show less
Authors A. Katharina Ceranski, Martha J. Carreño-Gonzalez, Anna C. Ehlers, ..., Florencia Cidre-Aranaz, Almut Schulze, € newald Thomas G.P. Gru Correspondence t.gruenewald@kitz-heidelberg.de In brief Show more
Authors A. Katharina Ceranski, Martha J. Carreño-Gonzalez, Anna C. Ehlers, ..., Florencia Cidre-Aranaz, Almut Schulze, € newald Thomas G.P. Gru Correspondence t.gruenewald@kitz-heidelberg.de In brief Ceranski et al. report on a refined Ewing sarcoma cell culture method with increased physiological relevance that is technically simple and cost efficient. The enhanced in vitro modeling has broad applicability for improving the validity of experimental results. Highlights d Simple Ewing sarcoma (EwS) cell culture method with Show less
2025 · Chemical Science · Royal Society of Chemistry · added 2026-04-21
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 kinase Show more
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
BACKGROUND: Drug repositioning is a pivotal strategy in pharmaceutical research, offering accelerated and cost-effective therapeutic discovery. However, biomedical information relevant to drug reposit Show more
BACKGROUND: Drug repositioning is a pivotal strategy in pharmaceutical research, offering accelerated and cost-effective therapeutic discovery. However, biomedical information relevant to drug repositioning is often complex, dispersed, and underutilized due to limitations in traditional extraction methods, such as reliance on annotated data and poor generalizability. Large language models (LLMs) show promise but face challenges such as hallucinations and interpretability issues.
OBJECTIVE: This study proposed long chain-of-thought for drug repositioning knowledge extraction (LCoDR-KE), a lightweight and domain-specific framework to enhance LLMs' accuracy and adaptability in extracting structured biomedical knowledge for drug repositioning.
METHODS: A domain-specific schema defined 11 entities (eg, drug, disease) and 18 relationships (eg, treats, is biomarker of). Following the established schema architecture, we constructed automatic annotation based on 10,000 PubMed abstracts via chain-of-thought prompt engineering. A total of 1000 expert-validated abstracts were curated into a drug repositioning corpus, a high-quality specialized corpus, while the remaining entries were allocated for model training purposes. Then, the proposed LCoDR-KE framework combined supervised fine-tuning of the Qwen2.5-7B-Instruct model with reinforcement learning and dual-reward mechanisms. Performance was evaluated against state-of-the-art models (eg, conditional random fields, Bidirectional Encoder Representations From Transformers, BioBERT, Qwen2.5, DeepSeek-R1, OpenBioLLM-70B, and model variants) using precision, recall, and F1-score. In addition, the convergence of the training method was assessed by analyzing performance progression across iteration steps.
RESULTS: LCoDR-KE achieved an entity F1 of 81.46% (eg, drug 95.83%, disease 90.52%) and triplet F1 of 69.04%, outperforming traditional models and rivaling larger LLMs (DeepSeek-R1: entity F1=84.64%, triplet F1=69.02%). Ablation studies confirmed the contributions of supervised fine-tuning (8.61% and 20.70% F1 drop if removed) and reinforcement learning (6.09% and 14.09% F1 drop if removed). The training process demonstrated stable convergence, validated through iterative performance monitoring. Qualitative analysis of the model's chain-of-thought outputs showed that LCoDR-KE performed structured and schema-aware reasoning by validating entity types, rejecting incompatible relations, enforcing constraints, and generating compliant JSON. Error analysis revealed 4 main types of mistakes and challenges for further improvement.
CONCLUSIONS: LCoDR-KE enhances LLMs' domain-specific adaptability for drug repositioning by offering an open-source drug repositioning corpus and a long chain-of-thought framework based on a lightweight LLM model. This framework supports drug discovery and knowledge reasoning while providing scalable, interpretable solutions applicable to broader biomedical knowledge extraction tasks. Show less
Ferredoxins (FDXs) are evolutionarily conserved iron-sulfur (Fe-S) proteins that serve as master regulators of mitochondrial redox homeostasis, governing critical processes including electron transfer Show more
Ferredoxins (FDXs) are evolutionarily conserved iron-sulfur (Fe-S) proteins that serve as master regulators of mitochondrial redox homeostasis, governing critical processes including electron transfer, energy metabolism, Fe-S cluster biogenesis, and steroidogenesis. In humans, the mitochondrial isoforms FDX1 and FDX2 exhibit specialized yet complementary functions: FDX1 directs steroidogenesis, protein lipoylation, and copper redox cycling, while FDX2 is a core factor in Fe-S cluster assembly. Crucially, dysregulation of these proteins disrupts mitochondrial integrity, impairs redox balance, and activates multiple programmed cell death (PCD) pathways such as cuproptosis, ferroptosis, apoptosis, and autophagic cell death. This review systematically analyzes their isoform-specific roles in mitochondrial electron transport, Fe-S cluster dynamics, metabolic regulation, and summarizes major advances in understanding how FDX1 and FDX2 orchestrate mitochondrial-PCD crosstalk. The work further examines their critical functions in PCD execution, including FDX1-mediated cuproptosis through Cu+-dependent aggregation of lipoylated proteins and FDX2-deficiency-driven ferroptosis via Fe-S cluster collapse and iron overload. Disease mechanisms across multiple pathologies, including cancer, neurodegeneration, cardiovascular disease, endocrine disorders, and genetic syndromes, are explored, highlighting links to FDX dysfunction, with emerging therapeutic strategies targeting FDXs also addressed. By elucidating the synergistic roles of FDX1 and FDX2 as metabolic-death gatekeepers, this review establishes a foundation for developing isoform-targeted therapies against diverse pathologies. Show less
2025 · Molecular Cancer · BioMed Central · added 2026-04-21
Ferroptosis, the non-apoptotic, iron-dependent form of cell death is an unavoidable outcome and byproduct of cellular metabolism. Reactive oxygen species generation during metabolic activities transce Show more
Ferroptosis, the non-apoptotic, iron-dependent form of cell death is an unavoidable outcome and byproduct of cellular metabolism. Reactive oxygen species generation during metabolic activities transcends to Fe2+-induced lipid peroxidation, leading to ferroptosis. Cancer cells being highly metabolic are more prone to ferroptosis. However, their neoplastic nature enables them to bypass ferroptosis and become ferroptosis-resistant. The capability of cancer cells to reprogram its metabolic activities is one of its finest abilities to abort oxidative damage, and hence ferroptosis. Moreover, the reprogrammed metabolism of cancer cells, also associates with the radical trapping antioxidant Show less
In recent years, mostly spanning the past decade, the concept of immunometabolism has ushered with a novel perspective on carcinogenesis, tumor progression, and tumor response to therapy. It has becom Show more
In recent years, mostly spanning the past decade, the concept of immunometabolism has ushered with a novel perspective on carcinogenesis, tumor progression, and tumor response to therapy. It has become clear that the metabolic state of immune cells plays a significant role in shaping their antitumor or protumor activities within the cancer microenvironment. Consequently, the examination of tumor metabolic heterogeneity, including an exploration of immunometabolism, proves indispensable for enhancing prognostic tools and advancing the quest for personalized treatments. Here we have delved into how metabolic reprogramming profoundly influences the acquisition and maintenance of functional states, spanning from effector and cytotoxic profiles to regulatory and immunosuppressive phenotypes in both innate and adaptive immunity. These alterations wield considerable influence over tumor evolution and affect the outcome of cancer. Furthermore, we explore some of the cellular signaling mechanisms that underpin the metabolic and phenotypic flexibility of immune cells in response to external stimuli. Show less