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Cancer remains a major global health burden, with rising incidence and mortality linked to aging populations and increased exposure to genotoxic agents. Oxidative stress plays a critical role in cancer development, progression, and resistance to therapy. The nuclear factor erythroid 2-related factor 2 (NRF2)-Kelch-like ECH-associated protein 1 (KEAP1)-antioxidant response element (ARE) signaling pathway is central to maintaining redox balance by regulating the expression of antioxidant and detoxification genes. Under physiological conditions, this pathway protects cells from oxidative damage, however, sustained activation of NRF2 in cancer, often due to mutations in KEAP1, supports tumor cell survival, drug resistance, and metabolic reprogramming. Recent studies demonstrate that NRF2 enhances glutathione (GSH) synthesis, induces detoxifying enzymes, and upregulates drug efflux transporters, collectively contributing to resistance against chemotherapy and targeted therapies. The inhibition of NRF2 using small molecules or dietary phytochemicals has shown promise in restoring drug sensitivity in preclinical cancer models. This review highlights the dual role of NRF2 in redox regulation and cancer therapy, emphasizing its potential as a therapeutic target. While targeting NRF2 offers a novel approach to overcoming treatment resistance, further research is needed to enhance specificity and facilitate clinical translation. 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, 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

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

Over the past decade, collective intelligence, i.e., the intelligence that emerges from collective efforts, has transformed complex problem-solving and decision-making. In drug discovery, decision-making often relies on medicinal chemistry intuition. The present study explores the application of collective intelligence in drug discovery, focusing on lead optimization. Ninety-two Sanofi researchers with diverse expertise participated anonymously in an exercise centered on ADMET-related questions. Their feedback was used to build a collective intelligence agent, which was compared to an artificial intelligence model. The study led to three major conclusions: first, collective intelligence improves decision-making in optimizing ADMET endpoints, compared to individual decisions. Second, collective intelligence outperforms artificial intelligence for all other endpoints but hERG inhibition. Finally, we observe complementarity between collective human and artificial intelligence. Overall, this research highlights the potential of collective intelligence in drug discovery and the importance of a synergistic approach combining human and artificial intelligence in project decision making. Show less

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

AbstractGold(III) complexes have garnered increasing attention in drug delivery due to their structural and mechanistic similarities to cisplatin. This study investigates an indazole‐based gold(III) carboxamide pincer complex, [N2·N6‐bis(1‐methyl‐1H‐indazol‐3‐yl)pyridine‐2·6‐dicarboxamide]gold(III) chloride (AuL), for its potential as an anticancer agent. Speciation analysis at physiological pH revealed that AuL predominantly exists as a neutral chlorinated species. The complex exhibited strong cytotoxicity against the MCF‐7 breast cancer cell line, with an impressive IC50 value of 9 µM, while showing no significant activity against the HT‐29 colon cancer cell line. Comprehensive analysis using electrophoresis, viscometry, ultraviolet‐visible spectroscopy (UV‐Vis), circular dichroism (CD), linear dichroism (LD) spectroscopy, and biomolecular simulations demonstrated that AuL binds to DNA via a dual mechanism, specifically minor groove binding and alkylation, with binding constants Ka1 = 1.48 × 109 M−1 and Ka2 = 6.59 × 105 M−1, respectively. Our data indicate that AuL initially binds to the minor groove of DNA, at which point a nucleobase substitutes the Cl ion, resulting in AuL binding directly to the DNA bases. In conclusion, the dual binding mode of AuL with DNA underscores its potential as a promising anticancer agent, opening new avenues for drug discovery and the development of metal‐based therapeutics. Show less

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

AuL4 triggers necroptosis and paraptosis in A549 cells. TLDR: AuL4 emerged as the most active compound, exhibited potent anticancer activity, triggering mitochondrial membrane depolarization and inducing necroptosis and paraptosis in human lung adenocarcinoma cells-a mechanism distinct from conventional apoptosis-inducing gold complexes. Show less

In this Review, Emerling and colleagues summarize the roles of phosphatidylinositol 4-kinases (PI4Ks) and phosphatidylinositol phosphate kinases (PIPKs) in cancer. They highlight the altered expression of these kinases in tumours and discuss ongoing efforts in developing therapies targeting these lesser-studied phosphoinositide kinase families. Show less

Computational metabolomics will be established in drug discovery and research on complex biological networks. This field of research enhances the detection of metabolic biomarkers and the prediction of molecular interactions by combining multiscale analysis with in silico and molecular docking methods. These include nuclear magnetic resonance, mass spectrometry, and innovative bioinformatics, which enable the accurate generation and characterization of metabolomes. Molecular docking is a crucial tool for simulating the interaction between ligands and receptors, thereby facilitating the identification of potential therapeutics. It also discusses the potential of metabolomics to inform drug modes of action, from pharmacokinetics to forecasting toxicity, thereby streamlining drug development pipelines. We highlight applications in anticancer, antimicrobial, and antiviral drug discovery and explain how these computational models can accelerate target validation and enhance the accuracy of therapeutic strategies. In addition, this review addresses the current challenges and future directions for computational techniques in conjunction with experimental data to advance personalized medicine. In conclusion, this review aims to highlight the prospective approaches of computational metabolomics and molecular docking that identify evolutionary adaptive metabolisms of multiscale biological systems through their synergistic utilization to overcome the key hurdles involved in both drug discovery and metabolomic research. Show less

Platinum-based drugs are a mainstay in chemotherapy, with traditional forms exerting their work directly on DNA. In recent years, it has been observed that platinum complexes had the potential to induce immunogenic cell death (ICD) and effectively trigger antitumor immune responses. Herein, to obtain novel platinum complexes with chemo-immunological properties, a series of Pt(ΙΙ)-N-heterocyclic carbene (Pt(ΙΙ)-NHC) complexes derived from 4,5-diarylimidazoles were synthesized. Among them, the dominant complex 3f was proved to exhibit better anti-liver cancer capacity compared to cisplatin and oxaliplatin. Complex 3f showed the ability to cause DNA damage by binding to DNA. In addition, it triggered intracellular reactive oxygen species (ROS) generation, affected the function of mitochondria, and blocked cells in G0/G1 phase, ultimately induced apoptosis in liver cancer cells. Furthermore, complex 3f activated endoplasmic reticulum stress (ERS) which promoted the release of damage-associated molecular patterns (DAMPs), induced ICD and dendritic cells (DCs) maturation. Interestingly, complex 3f also upregulated PD-L1, consequently converted "cold tumors" into "hot tumors". Overall, complex 3f had the potential to be regarded as a promising chemoimmunotherapy for the treatment of liver cancer. Show less

Computational drug discovery is essential for screening potential treatments and reducing the costs and time associated with proposing or combining drugs for disease management. Despite the extensive research conducted in this field, it remains an emerging area, particularly with the advent of machine learning, deep learning, and large language models (LLMs). This systematic review examines the integration of machine learning and deep learning techniques in drug discovery, concentrating on three critical areas: drug-drug interactions (DDIs), drug-target interactions (DTIs), and adverse drug reactions (ADRs). The review analyzes over 100 papers published between 2020 and 2025, categorizing the methods into deep learning, machine learning, graph learning, and hybrid models. It highlights the transformative impact of natural language processing (NLP) and LLMs in extracting meaningful insights from biomedical literature and chemical data. Furthermore, this work introduces key databases and data sets widely utilized in drug discovery. Additionally, this review identifies gaps in the existing research, such as the lack of comprehensive studies that simultaneously address DDI, DTI, and ADR extraction, and it proposes a more holistic approach to fill these gaps. The paper concludes by thoroughly evaluating various models, underscoring their performance metrics. 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

[Ru(bpy)₃]²⁺, tris(bipyridine)ruthenium(II), is a popular transition metal complex whose favorable photophysical properties have afforded it a central place in inorganic photochemistry and various related fields. In this perspective, in contrast to the large number of extant technical reviews, we instead note critical developments from a historical context. Of particular note are relatively lesser-known investigations in the field of analytical chemistry that predate the complex's rise to prominence as a photosensitizer. Recent studies that revisit the complex's own fundamental photophysics are also highlighted. Thus, in addition to serving as a proverbial almanac for the complex's rich history, this condensed perspective portends yet more fruitful lives for research into [Ru(bpy)₃]²⁺, despite the many already lived. 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 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

Influenza A viruses (IAVs) are single-stranded negative-sense RNA viruses that continually challenge animal and human health. In IAV-infected cells, host RNA-binding proteins play key roles in the life cycle of IAV by directly binding to viral RNA. Here, we examined the role of the host RNA-binding protein nucleophosmin-1 (NPM1) in IAV replication. We found that, as a nucleolar phosphoprotein, NPM1 directly binds to viral RNA (vRNA) and inhibits the replication of various subtypes of IAV. NPM1 binding to vRNA competitively reduces the assembly of the viral ribonucleoprotein complex and the viral polymerase activity, thereby reducing the generation of progeny viral RNA and virions. The RNA-binding activity of NPM1, with the key residues T199, T219, T234, and T237, is essential for its anti-influenza function. Taken together, our findings demonstrate that NPM1 acts as an RNA-binding protein and interacts with IAV vRNA to suppress viral replication. Show less

Academic Editor: Dooil Jeoung Received: 5 November 2025 Revised: 24 November 2025 Accepted: 26 November 2025 Published: 28 November 2025 Citation: Lee, J.; Roh, J.-L. Dihydroorotate Dehydrogenase in Mitochondrial Ferroptosis and Cancer Therapy. Cells 2025, 14, 1889. https://doi.org/10.3390/ cells14231889 Show less

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

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

Accurate oxygen detection and measurement of its concentration is vital in biological and industrial applications, necessitating highly sensitive and reliable sensors. Optical sensors, valued for their real-time monitoring, nondestructive analysis, and exceptional sensitivity, are particularly suited for precise oxygen measurements. Here, we report a dual-emissive iridium(III) complex, IrNPh₂, featuring "aggregation-induced emission" (AIE) properties and used for sensitive oxygen sensing. IrNPh₂ exhibits dual emissions at 450 and 515 nm, with 515 nm triplet-state emission demonstrating remarkable oxygen sensitivity due to its long-lived excited state (12.12 μs) and high quantum yield (68%). Stern-Volmer analysis reveals a notable quenching constant (K_sv = 12.44%^-1) and an ultralow detection limit of 0.0397%, emphasizing its superior performance. The oxygen quenching mechanism is driven by electron transfer (ET), supported by computational studies showing the lowest-unoccupied molecular orbital (LUMO) alignment of IrNPh₂ with the π_g^* orbitals of triplet oxygen, leading to superoxide radical (O₂^•-) formation. Electron paramagnetic resonance (EPR) studies further confirm this pathway. Biological evaluations using a three-dimensional (3D) U87-MG glioma spheroid model highlight the ability of IrNPh₂ to detect hypoxic regions, with significant fluorescence enhancement under hypoxia and minimal cytotoxicity (>80% viability at 100 μM). With high sensitivity, low detection limits, and biocompatibility, IrNPh₂ emerges as a promising candidate for oxygen sensing in environmental and biomedical applications, especially tumor hypoxia detection. Show less

Colorectal cancer (CRC) remains a significant global health challenge, ranking third in incidence and second in mortality among cancers worldwide. This review addresses the complex landscape of CRC, focusing on incidence, mortality trends, preventive strategies, and the evolving therapeutic approaches, particularly highlighting the role of platinum-based drugs like oxaliplatin (OXP). It also underscores the increasing burden of CRC, with factors such as westernized diets, aging populations, and genetic predispositions contributing to its prevalence. Therapeutically, early detection greatly enhances survival rates, emphasizing the importance of regular colonoscopies and stool tests. For advanced CRC, chemotherapy remains pivotal, with OXP as a cornerstone treatment despite its associated chemotherapy-induced peripheral neurotoxicity (CIPN). The review explores innovative strategies to overcome challenges related to chemotherapy, such as drug resistance and side effects, highlighting recent developments in the field, such as Pt(IV) prodrugs and immunotherapeutic approaches to enhance efficacy while minimizing toxicity. Additionally, this manuscript examines experimental models for drug screening, emphasizing the role of murine models and advanced 3D in vitro systems in CRC research. Overall, the review advocates for a comprehensive approach, integrating prevention, early detection, and personalized treatments to alleviate the global burden of CRC. 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

Conformer generation is crucial for computational chemistry tasks such as structure-based modeling and property prediction. Although reliable methods exist for organic molecules, coordination complexes remain challenging due to their diverse coordination geometries, ligand types, and stereochemistry. Current tools often lack the flexibility and reliability required for these systems. Here, we introduce MetalloGen, a novel algorithm designed for the automated generation of 3D conformers of mononuclear coordination complexes. MetalloGen accepts either SMILES strings or molecular graph representations as input and enables the generation of reliable conformers, including those with multiple polyhapto ligands, which are typically inaccessible to conventional conformer generators. To rigorously assess MetalloGen's performance, we benchmarked it on three distinct data sets: a curated collection of experimentally determined structures from the Cambridge Structural Database, the MOR41 benchmark set encompassing a wide range of organometallic reactions and complex ligand environments, and three catalytic reactions. Across all test sets, MetalloGen consistently reproduced appropriate geometries with high fidelity and demonstrated robust stereochemical control, even for challenging cases involving multiple polyhapto ligands. The versatility and reliability of MetalloGen make it a valuable tool for more accurate and efficient computational investigations in inorganic and organometallic chemistry. Show less

Cytochrome c (Cytc) is a multifunctional protein, essential for respiration and intrinsic apoptosis. Post-translational modifications of Cytc have been linked to physiological and pathophysiologic conditions, including cancer. Cytc tyrosine 67 (Y67) is a conserved residue that is important to the structure and function of Cytc. We here report the phosphorylation of Y67 of Cytc purified from bovine heart mapped by mass spectrometry. We characterized the functional effects of Y67 Cytc modification using in vitro and cell culture models. Y67 was mutated to the phosphomimetic glutamate (Y67E) and to phenylalanyl (Y67F) as a control. The phosphomimetic Y67E Cytc inhibited cytochrome c oxidase (COX) activity, redirecting energy metabolism toward glycolysis, and decreased the pro-apoptotic capabilities of Cytc. The phosphomimetic Y67E Cytc showed a significantly impaired rate of superoxide scavenging and a reduced rate of oxidation by hydrogen peroxide, suggesting a lower ability to transfer electrons and scavenge reactive oxygen species (ROS). Phosphomimetic Y67E replacement led to an almost complete loss of cardiolipin peroxidase activity, pointing to a central role of Y67 for this catalytic function of Cytc. In intact cells, phosphomimetic replacement leads to a reduction in cell respiration, mitochondrial membrane potential, and ROS levels. We propose that Y67 phosphorylation is cardioprotective and promotes cell survival. 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