📋 Browse Articles

TLDR: Investigation of anticancer and antitrypanosomatid activities of eight monoanionic metal bis(dithiolene) complexes showed that [Ph4P][Pt(tBu-thiazdt)2] and [Ph4P][Pd(tBu-thiazdt)2] complexes might have potential as novel anticancer and antitrypanosomatid agents as alternatives to current therapeutics. Show less

The double-stranded RNA editing enzyme ADAR1 connects two forms of genetic programming, one based on codons and the other on flipons. ADAR1 recodes codons in pre-mRNA by deaminating adenosine to form inosine, which is translated as guanosine. ADAR1 also plays essential roles in the immune defense against viruses and cancers by recognizing left-handed Z-DNA and Z-RNA (collectively called ZNA). Here, we review various aspects of ADAR1 biology, starting with codons and progressing to flipons. ADAR1 has two major isoforms, with the p110 protein lacking the p150 Zα domain that binds ZNAs with high affinity. The p150 isoform is induced by interferon and targets ALU inverted repeats, a class of endogenous retroelement that promotes their transcription and retrotransposition by incorporating Z-flipons that encode ZNAs and G-flipons that form G-quadruplexes (GQ). Both p150 and p110 include the Zβ domain that is related to Zα but does not bind ZNAs. Here we report strong evidence that Zβ binds the GQ that are formed co-transcriptionally by ALU repeats and within R-loops. By binding GQ, ADAR1 suppresses ALU-mediated alternative splicing, generates most of the reported nonsynonymous edits and promotes R-loop resolution. The recognition of the various alternative nucleic acid conformations by ADAR1 connects genetic programming by flipons with the encoding of information by codons. The findings suggest that incorporating G-flipons into editmers might improve the therapeutic editing efficacy of ADAR1. Show less

Carnitine O-acetyltransferase (CRAT) is a key mitochondrial enzyme involved in maintaining metabolic homeostasis by mediating the reversible transfer of acetyl groups between acetyl-CoA and carnitine. This enzymatic activity ensures the optimal functioning of mitochondrial carbon flux by preventing acetyl-CoA accumulation, buffering metabolic flexibility, and regulating the balance between fatty acid and glucose oxidation. CRAT’s interplay with the mitochondrial carnitine shuttle, involving carnitine palmitoyltransferases (CPT1 and CPT2) and the carnitine carrier (SLC25A20), underscores its critical role in energy metabolism. Emerging evidence highlights the structural and functional diversity of CRAT and structurally related acetyltransferases across cellular compartments, illustrating their coordinated role in lipid metabolism, amino acid catabolism, and mitochondrial bioenergetics. Moreover, the structural insights into CRAT have paved the way for understanding its regulation and identifying potential modulators with therapeutic applications for diseases such as diabetes, mitochondrial disorders, and cancer. This review examines CRAT’s structural and functional aspects, its relationships with carnitine shuttle members and other carnitine acyltransferases, and its broader role in metabolic health and disease. The potential for targeting CRAT and its associated pathways offers promising avenues for therapeutic interventions aimed at restoring metabolic equilibrium and addressing metabolic dysfunction in disease states. 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 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

Cancer cells often upregulate ribosome biogenesis to meet increased protein synthesis demands for rapid proliferation; therefore, targeting ribosome biogenesis has emerged as a promising cancer therapeutic strategy. Herein, we introduce two Pt complexes, ataluren monosubstituted platinum(IV) (SPA, formula: c,c,t,-[Pt(NH₃)₂Cl₂(OH)(C₁₅H₈FN₂O₃)], where C₁₅H₈FN₂O₃ = ataluren) and ataluren bisubstituted platinum(IV) complex (DPA, formula: c,c,t,-[Pt(NH₃)₂Cl₂(C₁₅H₈FN₂O₃)₂], where C₁₅H₈FN₂O₃ = ataluren), which effectively suppress ribosome biogenesis by inhibiting 47s pre-RNA expression. Furthermore, SPA and DPA induce nucleolar stress by dispersing nucleolar protein NPM1, ultimately inhibiting protein generation in tumor cells. More importantly, DPA exhibits superior cytotoxicity to various cancer cells and in vivo antitumor efficacy compared to cisplatin, with lower systemic toxicity. Notably, in clinically relevant models, including orthotopic hepatic tumor-bearing mice and patient-derived bladder cancer organoids, DPA outperforms cisplatin significantly, with the added benefit of oral administration, enhancing clinical feasibility. To our knowledge, DPA emerges as the pioneering Pt(IV) agent targeting the ribosome, providing new insights for designing next-generation metal-based therapeutics. Show less

Antimicrobial molecule discovered in soil from lab technician’s garden — plus, a huge study assessing the nuances of humans’ impacts on biodiversity. Hear the biggest stories from the world of science | 26 March 2025 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

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

Intracellular imaging of anticancer metallodrugs often relies on prelabeling with organic fluorophores, which significantly affects their physicochemical properties and intracellular distribution. On the other hand, the reported postlabeling strategies based on click-chemistry reactions require cell fixation and permeabilization. Here, this study presents a postlabeling approach based on the catalyst-free, inverse electron-demand Diels-Alder reaction (iEDDA) between a strained fluorescein-tagged bicyclononyne derivative (BCN-FAM) and half-sandwich Ir(III) complexes containing bidentate ligands comprising a tetrazine (Tz-R,R') entity. Five half-sandwich Ir(III) complexes with formula [Cp*Ir(Tz-R,R')Cl]^0/+ have been synthesized and fully characterized, including the X-ray crystal structures of three of the five derivatives. Investigations of their stability and their reactivity in aqueous solution and in a model iEDDA reaction reveal the strong influence of the tetrazine ligand structure on the chemical properties of the corresponding complexes. A highly cytotoxic metallodrug candidate (Ir-C,N_Ph,Me) is identified from biological studies, and chemical reactivity studies disclose an unusual preference for binding of methionine over cysteine. Postlabeling of Ir-C,N_Ph,Me in live HeLa cells highlights its preferential accumulation within the nucleus, suggesting its retention through covalent modifications of nuclear proteins in good agreement with other half-sandwich iridium(III) complexes. 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

ABSTRACTThe nucleolus, a prominent membrane‐less nuclear compartment, is organized around ribosomal RNA (rRNA) gene (rDNA) clusters, known as nucleolar organizing regions (NORs), located on the short arms of acrocentric chromosomes. It serves as the primary site for ribosome biogenesis, an energy‐intensive process crucial for cell growth and proliferation. This involves RNA polymerase I (Pol I)‐mediated transcription of 47S precursor rRNA (pre‐rRNA), pre‐rRNA processing, and ribosomal subunit assembly, reflected in its tripartite structure maintained by liquid–liquid phase separation. Recent evidence indicates that only about 30% of nucleolar proteins are exclusively involved in ribosome production. The remaining proteome participates in diverse cellular functions, establishing the nucleolus as a multifunctional organelle. It functions as a critical stress sensor and signaling hub, responding to various intracellular insults such as nutrient starvation, DNA damage, and viral infection. Many chemotherapeutic agents also induce the response called nucleolar stress via disruption of the nucleolar structure or function, potentially leading to rDNA instability. Nucleolar stress frequently leads to dynamic transition of nucleolar proteins, inducing nucleolar reorganization. Of these, the stress induced by transcriptional changes leads to the unique nucleolar structures termed nucleolar caps and nucleolar necklaces. In this review, we summarize the recent findings about the molecular mechanism of nucleolar changes upon stresses and discuss the possible relationship between rDNA instability and cancer. Show less

Significant progress has been made in understanding the mechanism of transcription-coupled nucleotide excision repair (TC-NER); however, numerous aspects remain elusive, including TC-NER regulation, lesion-specific and cell type-specific complex composition, structural insights, and lesion removal dynamics in living cells. This review summarizes and discusses recent advancements in TC-NER, focusing on newly identified interactors, mechanistic insights from cryo-electron microscopy (Cryo-EM) studies and live cell imaging, and the contribution of post-translational modifications (PTMs), such as ubiquitin, in regulating TC-NER. Furthermore, we elaborate on the consequences of TC-NER deficiencies and address the role of accumulated damage and persistent lesion-stalled RNA polymerase II (Pol II) as major drivers of the disease phenotype of Cockayne syndrome (CS) and its related disorders. In this context, we also discuss the severe effects of transcription-blocking lesions (TBLs) on neurons, highlighting their susceptibility to damage. Lastly, we explore the potential of investigating three-dimensional (3D) chromatin structure and phase separation to uncover further insights into this essential DNA repair pathway. Show less

Small redox active molecules such as reactive nitrogen and oxygen species and hydrogen sulfide have emerged as important biological mediators that are involved in various physiological and pathophysiological processes. Advancement in understanding of cellular mechanisms that tightly regulate both generation and reactivity of these molecules is central to improved management of various disease states including cancer and cardiovascular dysfunction. Imbalance in the production of redox active molecules can lead to damage of critical cellular components such as cell membranes, proteins and DNA and thus may trigger the onset of disease. These small inorganic molecules react independently as well as in a concerted manner to mediate physiological responses. This review provides a general overview of the redox biology of these key molecules, their diverse chemistry relevant to physiological processes and their interrelated nature in cellular signaling. Show less

The coordination capacity of thiosemicarbazone ligands and their synergism with palladium(II) ions modulate their reactivity, allowing custom design. Using thiosemicarbazones with two potential stable tautomeric forms and imidazole as bioisosteres, we studied how the substitution in the N4 group of the thiosemicarbazone by the p-chlorophenyl group modifies their hydrophilic properties, integrity in solution, and interactions toward their potential targets. The coordination to Pd(II) affects the bioactivity of the ligands, resulting in either improved or reduced antiproliferative effects depending on the cell type (cancerous versus bacterial, respectively). Show less

Differential and even opposing functions of two major antioxidant transcription factors Nrf1 and Nrf2 (encoded by Nfe2l1 and Nfe2l2, respectively) are determined by distinctions in their tempospatial positioning, topological repartitioning, proteolytic processing, and biochemical modification, as well as in their shared evolutionary origin. As a matter of fact, the allelopathic potentials of Nrf1 and Nrf2 (both resembling two entangled 'Yin-Yang' quanta that comply with a dialectic law of the unity of opposites) are fulfilled to coordinately control redox physiological homeostasis so as to be maintained within the presetting thresholds. By putative exponential curves of redox stress and intrinsic anti-redox capability, there is inferable to exist a set point at approaching zero with the 'Golden Mean' for the healthy survival (i.e., dubbed the 'zero theory'). A bulk of the hitherto accumulating evidence demonstrates that the set point of redox homeostasis is dictated selectively by multi-hierarchical threshold settings, in which the living fossil-like Nrf1 acts as a robust indispensable determinon, whereas Nrf2 serves as a versatile chameleon-like master regulon, in governing the redox homeodynamic ranges. This is attributable to the facts that Nrf2 has exerted certain 'double-edged sword' effects on life process, whereas Nrf1 executes its essential physiobiological functions, along with unique pathophysiological phenotypes, by integrating its 'three-in-one' roles elicited as a specific triplet of direct sensor, transducer and effector within multi-hierarchical stress responsive signaling to redox metabolism and target gene reprogramming. Here, we also critically reviewed redox regulation of physio-pathological functions from the eco-evo-devo perspectives, through those coding rules (redox code, stress-coping code, and topogenetic code). The evolving concepts on stress and redox stress were also further revisited by scientific principles of physics and chemistry. Besides, several novel concepts such as oncoprotists, Reverse Central Dogma, and Grand Redox-Unifying Theory' (GRUT) of life, together with diffusive reactive species (DRS)-based murburn concept integrating all stochastic electron-, proton- and/or moiety-transfer reactive and interactive processes (e.g., PCHEMS), are introduced in this interdisciplinary and synthetic review. Show less

In this study, the changes in the DNA native conformation induced by pH changes in the alkaline and acidic regions were examined. It was shown by the methods of low gradient viscometry and flow birefringence that protonation and deprotonation of nitrogen bases inside the double helix cause a change in the persistent length of DNA. The pK values shift with the change in the ionic strength of the solution (NaCl concentration). The additional charges appearing on the DNA bases are not shielded by counterions from the solution. The increase and decrease in the volume of the DNA coil in solution resulting from protonation and deprotonation of base pairs, respectively, are mainly determined by changes in the persistent length of the macromolecule. The stability of the double-helical conformation of DNA ensures the steadiness of the equilibrium rigidity of this macromolecule. The emergence of charges on the bases, resulting from DNA protonation or deprotonation, weakens and even disrupts the hydrogen bonds between complementary bases. However, at the first stage, this occurs without altering the stacking interactions of base pairs, as reflected in the absorption spectra of DNA and in the stability of the DNA persistent length at different pH levels. 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 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

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

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

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

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

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