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Described are multiple approaches using density functional theory to probe the acid catalyzed aquation of the hexaammineruthenium(II) cation (Ru(NH₃)₆²⁺ + H₃O⁺ → Ru(NH₃)₅(H₂O)²⁺ + NH₄⁺) reported initially by Taube and co-workers. These computations support the proposal that the initial step is protonation of the Ru(II) center and/or the metal-NH₃ bond, thereby activating the latter toward dissociation. DFT analysis was also carried out for the hypothetical acid-mediated aquation of the isoelectronic hexaamminerhodium(III) complex, Rh(NH₃)₆³⁺. The computations suggest a key mechanistic difference for the latter pathway, namely that protonation of the NH₃ occurs late in a reaction coordinate involving dissociation of the Rh-NH₃ with no direct interaction of H⁺ with the metal center. Furthermore, while the calculated activation energy is considerably higher in the latter case, the calculations suggest that protonation could play an important role in such ligand substitution reactions. Show less

Drug resistance and distant metastases are leading causes of mortality in colorectal cancer (CRC), yet the molecular mechanisms linking these processes remain elusive. In this study, we demonstrate that acquired resistance to oxaliplatin, a first-line chemotherapeutic in CRC, enhances metastatic potential through transcriptional reprogramming. Using a clinically relevant dosing regimen, we generated oxaliplatin-resistant CRC cells that displayed increased metastatic potential. Integrated transcriptomic and phenotypic analyses revealed that dysregulated cholesterol biogenesis amplifies TGF-β signaling, which in turn drives expression of SERPINE1, which serves as a key effector of both oxaliplatin resistance and metastasis. Furthermore, we uncovered a SERPINE1-associated nine-gene expression signature, RESIST-M, that robustly predicts overall and relapse-free survival across distinct patient cohorts. Notably, RESIST-M stratifies a high-risk subtype of CMS4/iCMS3-fibrotic patients that display the poorest prognosis, underscoring its clinical relevance. Targeting of SERPINE1 or cholesterol biosynthesis re-sensitized resistant, pro-metastatic cells to oxaliplatin in mouse xenograft models. Altogether, this study uncovers a mechanistic link between metabolic rewiring and transcriptional plasticity underlying therapy-induced metastasis in primary CRC. Additionally, it also reveals actionable vulnerabilities that offer both prognostic value and therapeutic potential. Show less

Redox signaling acts as a critical mediator in the dynamic interactions between organisms and their external environment, profoundly influencing both the onset and progression of various diseases. Under physiological conditions, oxidative free radicals generated by the mitochondrial oxidative respiratory chain, endoplasmic reticulum, and NADPH oxidases can be effectively neutralized by NRF2-mediated antioxidant responses. These responses elevate the synthesis of superoxide dismutase (SOD), catalase, as well as key molecules like nicotinamide adenine dinucleotide phosphate (NADPH) and glutathione (GSH), thereby maintaining cellular redox homeostasis. Disruption of this finely tuned equilibrium is closely linked to the pathogenesis of a wide range of diseases. Recent advances have broadened our understanding of the molecular mechanisms underpinning this dysregulation, highlighting the pivotal roles of genomic instability, epigenetic modifications, protein degradation, and metabolic reprogramming. These findings provide a foundation for exploring redox regulation as a mechanistic basis for improving therapeutic strategies. While antioxidant-based therapies have shown early promise in conditions where oxidative stress plays a primary pathological role, their efficacy in diseases characterized by complex, multifactorial etiologies remains controversial. A deeper, context-specific understanding of redox signaling, particularly the roles of redox-sensitive proteins, is critical for designing targeted therapies aimed at re-establishing redox balance. Emerging small molecule inhibitors that target specific cysteine residues in redox-sensitive proteins have demonstrated promising preclinical outcomes, setting the stage for forthcoming clinical trials. In this review, we summarize our current understanding of the intricate relationship between oxidative stress and disease pathogenesis and also discuss how these insights can be leveraged to optimize therapeutic strategies in clinical practice. Show less

A fundamental biological mechanism, programmed cell death (PCD), is essential for tissue homeostasis, immunological control, and development. Its dysregulation is a characteristic of many diseases in multicellular organisms, including cancer, where unchecked proliferation is made possible by evading cell death. Therefore, one of the main tenets of contemporary anticancer therapies is the restoration or induction of PCD in cancer cells. One potential, least invasive method among these is photodynamic treatment (PDT). PDT uses light-activatable photosensitisers, which cause cancer cells to explode with reactive oxygen species (ROS) when exposed to light. These ROS harm important biomolecules, throw off the cellular redox equilibrium, and cause cells to die. PDT-induced cell death was previously believed to be mostly caused by autophagy, necrosis, or apoptosis. Recent research, however, has shown that it can trigger a wider range of unconventional cell death pathways. ROS can cause ferroptosis by oxidising membrane lipids, fragmenting DNA, and lowering intracellular glutathione (GSH) levels. Similarly, necroptosis or pyroptosis can result from severe oxidative stress activating death receptor signalling. Sometimes, in response, cells use survival strategies like autophagy, which can also lead to cell death. This review explores these new, unconventional methods of cell death and how PDT can be used to take advantage of them. Next-generation photosensitisers based on iridium (Ir), ruthenium (Ru), and rhenium (Re) complexes are given special attention because they provide deep tissue penetration, improved photostability, and adjustable ROS production. Their incorporation into PDT has revolutionary potential for improving cancer treatment precision and conquering therapeutic resistance. Show less

Morpholine motifs have been used extensively as targeting moieties for lysosomes, primarily in fluorescence imaging agents. Traditionally these imaging agents are based on organic molecules which have several shortcomings including small Stokes shifts, short emission lifetimes, and susceptibility to photobleaching. To explore alternative lysosome targeting imaging agents we have used a rhenium based phosphorescent platform which has been previously demonstrated to have an improved Stokes shift, a long lifetime emission, and is highly photostable. Rhenium complexes containing morpholine substituted ligands were designed to accumulate in acidic compartments. Two of the three complexes prepared exhibited bright emission in cells, when incubated at low concentrations (20 μM) and were non-toxic at concentrations as high as 100 μM, making them suitable for live cell imaging. We show that the rhenium complexes are amenable to chemical modification and that the morpholine targeted derivatives can be used for live cell confocal fluorescence imaging of endosomes–lysosomes. Show less

Esta macro infografía, es un conjunto de gráficos temáticos (12) que suman un relato visual informativo científico-criminalístico que se publicó hace 20 años en El Periódico de Catalunya a doble página, y no ha parado de crecer hasta hoy. En la primera parte se expone el proceso de trabajo, desde el intelectual hasta el gráfico. La línea narrativa muestra un escenario lleno de contradicciones, en donde se asesinó al presidente de EEUU, John Fitzgerald Kennedy, el 22 de noviembre del 1963. Ahora se cumplen 60 años. La infografía, ha sido corregida, retocada, cambiada, formateada, y puesta al día, en varias ocasiones, -aunque preservando el “look” del momento en que se hizo-, a causa de participar en conferencias, debates, simposiums, exposiciones, clases magistrales, y clases convencionales. La infografía JFK sirvió de base en la Escuela de Diseño EINA, para que los alumnos de Infografía realizasen excelentes trabajos, que merecieron el “European Newspaper Award”, de Mejor infografía de prensa 2014. Para mí, el principal principio científico de una buena infografía es que una información visual se ha entender y controlar muchísimo más ágilmente, que la misma información leída en un texto, o explicada oralmente. Y pienso que en este caso se consiguió. Lo que sigue muestra los esquemas que estructuran la infografía global, y el análisis de cada uno de los gráficos parciales, de sus herramientas de diseño infográfico, y también como portadores de contenidos informativos visuales. Anexos se presentan los materiales de investigación en formato pdf. También un un vídeo en formato .mov: https://youtu.be/flGWbTtWfrg Show less

Rhenium(I) tricarbonyl complexes are widely studied for their cell imaging properties and anti-cancer and anti-microbial activities, but the complexes with S-donor ligands remain relatively unexplored. A series of six fac-[Re(NN)(CO)3(SR)] complexes, where (NN) is 2,2′-bipyridyl (bipy) or 1,10-phenanthroline (phen), and RSH is a series of thiocarboxylic acid methyl esters, have been synthesized and characterized. Cellular uptake and anti-proliferative activities of these complexes in human breast cancer cell lines (MDA-MB-231 and MCF-7) were generally lower than those of the previously described fac-[Re(NN)(CO)3(OH2)]+ complexes; however, one of the complexes, fac-[Re(CO)3(phen)(SC(Ph)CH2C(O)OMe)] (3b), was active (IC50 ∼ 10 μM at 72 h treatment) in thiol-depleted MDA-MB-231 cells. Moreover, unlike fac-[Re(CO)3(phen)(OH2)]+, this complex did not lose activity in the presence of extracellular glutathione. Taken together these properties show promise for further development of 3b and its analogues as potential anti-cancer drugs for co-treatment with thiol-depleting agents. Conversely, the stable and non-toxic complex, fac-[Re(bipy)(CO)3(SC(Me)C(O)OMe)] (1a), predominantly localized in the lysosomes of MDA-MB-231 cells, as shown by live cell confocal microscopy (λex = 405 nm, λem = 470–570 nm). It is strongly localized in a subset of lysosomes (25 μM Re, 4 h treatment), as shown by co-localization with a Lysotracker dye. Longer treatment times with 1a (25 μM Re for 48 h) resulted in partial migration of the probe into the mitochondria, as shown by co-localization with a Mitotracker dye. These properties make complex 1a an attractive target for further development as an organelle probe for multimodal imaging, including phosphorescence, carbonyl tag for vibrational spectroscopy, and Re tag for X-ray fluorescence microscopy. Show less

AbstractThe reaction of Re(CO)5Br with deprotonated 1H‐(5‐(2,2′:6′,2′′‐terpyridine)pyrid‐2‐yl)tetrazole yields a triangular assembly formed by tricarbonyl Re(I) vertices. Photophysical measurements reveal blue‐green emission with a maximum at 520 nm, 32 % quantum yield, and 2430 ns long‐lived excited state decay lifetime in deaerated dichloromethane solution. Coordination of lanthanoid ions to the terpyridine units red‐shifts the emission to 570 nm and also reveals efficient (90 %) and fast sensitisation of both Eu(III) and Yb(III) at room temperature, with a similar rate constant kET on the order of 107 s−1. Efficient sensitisation of Eu(III) from Re(I) is unprecedented, especially when considering the close proximity in energy between the donor and acceptor excited states. On the other hand, comparative measurements at 77 K reveal that energy transfer to Yb(III) is two orders of magnitude slower than that to Eu(III). A two‐step mechanism of sensitisation is therefore proposed, whereby the rate‐determining step is a thermally activated energy transfer step between the Re(I) centre and the terpyridine functionality, followed by rapid energy transfer to the respective Ln(III) excited states. At 77 K, the direct Re(I) to Eu(III) energy transfer seems to proceed via a ligand‐mediated superexchange Dexter‐type mechanism. Show less

Interest in covalent enzyme inhibitors as therapeutic agents has seen a recent resurgence. Covalent enzyme inhibitors typically possess an organic functional group that reacts with a key feature of the target enzyme, often a nucleophilic cysteine residue. Herein, the application of small, modular Re^V complexes as inorganic cysteine-targeting warheads is described. These metal complexes were found to react with cysteine residues rapidly and selectively. To demonstrate the utility of these Re^V complexes, their reactivity with SARS-CoV-2-associated cysteine proteases is presented, including the SARS-CoV-2 main protease and papain-like protease and human enzymes cathepsin B and L. As all of these proteins are cysteine proteases, these enzymes were found to be inhibited by the Re^V complexes through the formation of adducts. These findings suggest that these Re^V complexes could be used as a new class of warheads for targeting surface accessible cysteine residues in disease-relevant target proteins. Show less

Twelve Re(I) tricarbonyl diimine (2,2′-bipyridine and 1,10-phenanthroline) complexes with thiotetrazolato ligands have been synthesised and fully characterised. Structural characterisation revealed the capacity of the tetrazolato ligand to bind to the Re(I) centre through either the S atom or the N atom with crystallography revealing most complexes being bound to the N atom. However, an example where the Re(I) centre is linked via the S atom has been identified. In solution, the complexes exist as an equilibrating mixture of linkage isomers, as suggested by comparison of their NMR spectra at room temperature and 373 K, as well as 2D exchange spectroscopy. The complexes are photoluminescent in fluid solution at room temperature, with emission either at 625 or 640 nm from the metal-to-ligand charge transfer excited states of triplet multiplicity, which seems to be exclusively dependent on the nature of the diimine ligand. The oxygen-sensitive excited state lifetime decay ranges between 12.5 and 27.5 ns for the complexes bound to 2,2′-bipyrdine, or between 130.6 and 155.2 ns for those bound to 1.10-phenanthroline. Quantum yields were measured within 0.4 and 1.5%. The complexes were incubated with human lung (A549), brain (T98g), and breast (MDA-MB-231) cancer cells, as well as with normal human skin fibroblasts (HFF-1), revealing low to moderate cytotoxicity, which for some compounds exceeded that of a standard anti-cancer drug, cisplatin. Low cytotoxicity combined with significant cellular uptake and photoluminescence properties provides potential for their use as cellular imaging agents. Furthermore, the complexes were assessed in disc diffusion and broth microdilution assays against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), Escherichia coli (E. coli), and Pseudomonas aeruginosa (P. aeruginosa) bacterial strains, which revealed negligible antibacterial activity in the dark or after irradiation. Show less

AbstractWell‐defined copolymers containing luminescent iridium and hybrid iridium/rhenium fragments are prepared utilizing parent poly(n‐butyl acrylamide‐co‐N‐(1H‐tetrazol‐5‐yl) acrylamide) as macromolecular chelating species. The parent (co)polymers are prepared via the modification of a precursor poly(pentafluorophenyl acrylate) (polyPFPA) homopolymer, prepared by reversible addition‐fragmentation chain transfer polymerization, with n‐butylamine and 5‐aminotetrazole. Reaction of the parent copolymers with [Ir2(ppy)4(μ−Cl2)] (ppy = 2‐phenylpyridine) yields modified copolymers containing the Ir(ppy)2 fragment as a pendent group. Attachment of the Ir species is confirmed by a combination of photophysical studies, UV–Vis spectroscopy, and visually under irradiation with UV light. Importantly, it is demonstrated that the chelation of the Ir(ppy)2 fragment to a polymeric scaffold does not impact the fundamental photophysical properties of the Ir species. Attachment of a second luminescent metal species, Re(CO)3(phen) (phen = 1,10‐phenanthroline), gives hybrid materials containing Re(I) and Ir(III). The photophysical properties of these hybrid materials are consistent with the presence of both metal species and indicate the occurrence of energy transfer phenomena from the polymer‐bound Ir to Re metal centers. Finally, it is demonstrated that the Ir modified polymers and the Ir/Re hybrid materials offer potential in tissue imaging applications with scope to tune both luminescent properties and biological specificity as evidenced from preliminary brain tissue staining experiments. Show less

Numerous colon cancer cases are resistant to chemotherapy based on oxaliplatin and suffer from relapse. A number of survival- and prognosis-related biomarkers have been identified based on database mining for patients who develop drug resistance, but the single individual gene biomarker can not attain high specificity and sensitiv-ity in prognosis predictionh. This work was conducted aiming to establish a new gene signature using oxaliplatin resistance-related genes to predict the prognosis for colon cancer. To this end, we downloaded gene expression profile data of cell lines resistant and not resistant to oxaliplatin from the Gene Expression Omnibus (GEO) database. Altogether 495 oxaliplatin resistance-related genes were searched by weighted gene co-expression network analysis (WGCNA) and differential expression analysis. As suggested by functional analysis, the above genes were mostly enriched into cell adhesion and immune processes. Besides, a signature was built based on 4 oxaliplatin resistance-related genes selected from training set to predict the overall survival (OS) by stepwise regression and least absolute shrinkage and selection op-erator (LASSO) Cox analysis. Relative to low risk score group, the high risk score group had dismal OS (P 0.7). Additionally, multivariate Cox regression suggested that, the signature constructed based on 4 oxaliplatin re-sistance-related genes predicted the prognosis for colon cancer cases (HR, 2.77; 95% CI, 2.03–3.78; P<0.001). Finally, external test sets were utilized to further validate the stability and accuracy of oxaliplatin resistance-related gene signature for prog-nosis of colon cancer patients. To sum up, this study establishes a signature based on 4 oxaliplatin resistance-related genes for predicting the survival of colon cancer pa-tients, which sheds more lights on the mechanisms of oxaliplatin resistance and helps to identify colon cancer cases with dismal prognostic outcome. Show less

The right-handed double-helical structure of DNA (B-DNA), which follows the Watson-Crick model, is the canonical form of DNA existing in normal physiological settings. Even though an alternative left-handed structure of DNA (Z-DNA) was discovered in the late 1970s, Z-form nucleic acid has not received much attention from biologists, because it is extremely unstable under physiological conditions, has an ill-defined mechanism of its formation, and has obscure biological functions. The debate about the physiological relevance of Z-DNA was settled only after a class of proteins was found to potentially recognize the Z-form architecture of DNA. Interestingly, these Z-DNA binding proteins can bind not only the left-handed form of DNA but also the equivalent structure of RNA (Z-RNA). The Z-DNA/RNA binding proteins present from viruses to humans function as important regulators of biological processes. In particular, the proteins ADAR1 and ZBP1 are currently being extensively re-evaluated in the field to understand potential roles of the noncanonical Z-conformation of nucleic acids in host immune responses and human disease. Despite a growing body of evidence supporting the biological importance of Z-DNA/RNA, there remain many unanswered principal questions, such as when Z-form nucleic acids arise and how they signal to downstream pathways. Understanding Z-DNA/RNA and the sensors in different pathophysiological conditions will widen our view on the regulation of immune responses and open a new door of opportunity to develop novel types of immunomodulatory therapeutic possibilities. [BMB Reports 2020; 53(9): 453-457]. Show less

The automatic recognition of chemical structure diagrams from the literature is an indispensable component of workflows to re-discover information about chemicals and to make it available in open-access databases. Here we report preliminary findings in our development of Deep lEarning for Chemical ImagE Recognition (DECIMER), a deep learning method based on existing show-and-tell deep neural networks, which makes very few assumptions about the structure of the underlying problem. It translates a bitmap image of a molecule, as found in publications, into a SMILES. The training state reported here does not yet rival the performance of existing traditional approaches, but we present evidence that our method will reach a comparable detection power with sufficient training time. Training success of DECIMER depends on the input data representation: DeepSMILES are superior over SMILES and we have a preliminary indication that the recently reported SELFIES outperform DeepSMILES. An extrapolation of our results towards larger training data sizes suggests that we might be able to achieve near-accurate prediction with 50 to 100 million training structures. This work is entirely based on open-source software and open data and is available to the general public for any purpose. Show less

AbstractThe exposure of phosphatidylserine (PS) on the outer plasma membrane has long been considered a unique feature of apoptotic cells. Together with other “eat me” signals, it enables the recognition and phagocytosis of dying cells (efferocytosis), helping to explain the immunologically-silent nature of apoptosis. Recently, however, PS exposure has also been reported in non-apoptotic forms of regulated inflammatory cell death, such as necroptosis, challenging previous dogma. In this review, we outline the evidence for PS exposure in non-apoptotic cells and extracellular vesicles (EVs), and discuss possible mechanisms based on our knowledge of apoptotic-PS exposure. In addition, we examine the outcomes of non-apoptotic PS exposure, including the reversibility of cell death, efferocytosis, and consequent inflammation. By examining PS biology, we challenge the established approach of distinguishing apoptosis from other cell death pathways by AnnexinV staining of PS externalization. Finally, we re-evaluate how PS exposure is thought to define apoptosis as an immunologically silent process distinct from other non-apoptotic and inflammatory cell death pathways. Ultimately, we suggest that a complete understanding of how regulated cell death processes affect the immune system is far from being fully elucidated.Graphical abstract Show less

Reactive Oxygen Species (ROS) can cause oxidative damage and have been proposed to be the main cause of ageing and age-related diseases including cancer, diabetes and Parkinson’s disease. Accordingly, mitochondria from old individuals have higher levels of ROS. However, ROS also participate in cellular signaling, are instrumental for several physiological processes and boosting ROS levels in model organisms extends lifespan. The current consensus is that low levels of ROS are beneficial, facilitating adaptation to stress via signalling, whereas high levels of ROS are deleterious because they trigger oxidative stress. Based on this model the amount of ROS should determine the physiological effect. However, recent data suggests that the site at which ROS are generated is also instrumental in determining effects on cellular homeostasis. The best example of site-specific ROS signaling is reverse electron transport (RET). RET is produced when electrons from ubiquinol are transferred back to respiratory complex I, reducing NAD+ to NADH. This process generates a significant amount of ROS. RET has been shown to be instrumental for the activation of macrophages in response to bacterial infection, re-organisation of the electron transport chain in response to changes in energy supply and adaptation of the carotid body to changes in oxygen levels. In Drosophila melanogaster, stimulating RET extends lifespan. Here, we review what is known about RET, as an example of site-specific ROS signaling, and its implications for the field of redox biology. Show less

Platinum compounds are a mainstay of cancer chemotherapy, with over 50% of patients receiving platinum. But there is a great need for improvement. Major features of the cisplatin mechanism of action involve cancer cell entry, formation mainly of intrastrand cross-links that bend and unwind nuclear DNA, transcription inhibition and induction of cell-death programmes while evading repair. Recently, we discovered that platinum cross-link formation is not essential for activity. Monofunctional Pt compounds such as phenanthriplatin, which make only a single bond to DNA nucleobases, can be far more active and effective against a range of tumour types. Without a cross-link-induced bend, monofunctional complexes can be accommodated in the major groove of DNA. Their biological mechanism of action is similar to that of cisplatin. These discoveries opened the door to a large family of heavy metal-based drug candidates, including those of Os and Re, as will be described. Show less