📋 Browse Articles

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

In this work, we present the bioorthogonal activation and mitochondria targeting of a near-infrared-emitting iridium(iii) nitrone complex via cyclooctynylated phosphonium cations for enhanced cellular imaging and photodynamic therapy. 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 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

The preparation of a new series of Ir(III) tetrazolato complexes with the general formula [Ir(C^N)2(N^N)]0/+, where the ancillary ligand (N^N) is represented in turn by 2-pyridyltetrazolato (PTZ-), 2-pyrazinyltetrazolato (PYZ-) or 2-pyridyl 5-trifluoromethyl tetrazolato (PTZ-CF3-), is described herein. The design of the cyclometalated (C^N) ligands, namely 2-phenylisonicotinonitrile (ppyCN) and 2-(2,4-difluorophenyl)isonicotinonitrile (F2ppy-CN), features the well-known ppy- or F2ppy core, with the introduction of one electron-withdrawing cyano (-CN) group at the para position of the pyridyl ring. The photophysical and electrochemical properties of the new Ir(III) cyclometalated complexes have been investigated and the resulting data suggest how the (C^N) ligands significantly rule the luminescence behavior of the new complexes. Further blue or red shifting of the emission profiles of the neutral complexes was observed upon their conversion into cationic species through the regioselective addition of a methyl moiety to the coordinated tetrazolato ring. Lastly, neutral [Ir(F2ppy-CN)2(PTZ)] was used as an emissive phosphor for the fabrication of an OLED-type device. 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

This study presents a protein search framework with conformal prediction, enabling statistically reliable annotation of protein function. The method improves homology search, enzyme classification, and filters proteins for further characterization. Show less

Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein question answering systems. To tackle these issues, we propose the Prot2Chat framework. Show less

Abstract Background: Chemoresistance remains a significant barrier in colorectal cancer (CRC) treatment, particularly with oxaliplatin, a key first-line chemotherapy agent. This study is therefore aimed to develop an in vitro model of oxaliplatin-resistant HCT116 cells and investigate the associated morphological and molecular adaptations to identify potential dysregulated survival and apoptotic pathways that are playing a role in developing chemoresistance. Methods: HCT116 CRC cells were cultured, and resistance was induced by stepwise oxaliplatin exposure, with recovery phases between treatments. Morphological changes during resistance development were observed using phase-contrast microscopy. Flow cytometry was performed to analyze cell cycle distribution and apoptotic cell populations. Gene expression of key survival pathways, including Wnt/β-catenin, NFκB, and PI3K/Akt, was assessed using qPCR to identify molecular alterations associated with resistance. Results: Parental HCT116 cells displayed cuboidal morphology, high proliferation (Ki-67 positivity), and epithelial characteristics (moderate E-cadherin and ALDH1 expression). Resistant cells exhibited increased morphological heterogeneity, cell detachment, and features of epithelial-mesenchymal transition (EMT). Flow cytometry revealed a significant reduction in the sub-G1 population and an increase in the G2/M phase, suggesting diminished apoptosis and cell cycle dysregulation in oxaliplatin resistant HCT116 cells as compared to wild type. Gene expression analysis showed a marked upregulation of β-catenin, NFκB, and PI3K/Akt pathway components, coupled with increased expression of EMT markers (Snail, Vimentin) and drug efflux genes (ABCG2, ABCC1) in oxaliplatin resistant cells as compared to wild type HCT116 cells suggesting a role of these survival pathways and genes in induction of resistance. Conclusion: Oxaliplatin resistance in HCT116 CRC cells is characterized by morphological plasticity, altered cell cycle regulation, and activation of survival pathways, including Wnt/β-catenin, NFκB, and PI3K/Akt. These findings highlight the complexity of chemoresistance and provide a basis for identifying novel targets to enhance treatment efficacy in CRC. Citation Format: Aliza Jafri, Sheerien Rajput, Areeb Ahmed, Azhar Hussain Rajabali, Kulsoom Ghias. Identification of signaling and apoptotic pathway alterations in oxaliplatin resistant HCT116 colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl₁₎:Abstract nr 4417. 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

Traditional protein engineering methods are often slow and labor-intensive. Here, authors develop an automatic protein evolution platform enabled by a protein language model. Using this platform, they significantly improved the activity of a tRNA synthetase within ten days. 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

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

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

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

In this work, we have carefully designed and synthesized two Ru(II) metal complexes: [Ru(phen)₂(HMPIP)](PF₆)₂ (6a, where phen = 1,10-phenanthroline, HMPIP = 2-(2-hydroxy-3-methylphenyl-1H-imidazo[4,5-f][1,10]phenanthroline) and [Ru(bpy)₂(HMPIP)](PF₆)₂ (6b, where bpy = 2,2'-bipyridine). Using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to explore the cytotoxicity of 6a and 6b towards HepG2, B16, A549, SGC-7901, HCT116 and non-cancer LO2. The complexes exhibited cytotoxicity activity against HepG2 cells. The capacity of 6a and 6b to impede the proliferation and dissemination of cancer cells was evaluated by conducting proliferation and migration experiments and 3D model. The anticancer mechanism was investigated in detail. The utilization of cycle blocking assays revealed that 6a and 6b induced a G0/G1 phase arrest in HepG2 cells. The cellular uptake experiments show that the complexes enter the cell nuclei, then escape from the cell nuclei into the cytoplasm, finally accumulate in the mitochondria. Apoptosis assays and the examination of proteins indicated that the complexes were capable of efficiently inducing apoptosis in HepG2 cells. Additionally, the potential induction of autophagy-mediated cell death was explored. The observed reduction in glutathione (GSH) levels and glutathione peroxidase 4 (GPX4) expression suggested a disruption of redox homeostasis within cancer cells, an increment in malondialdehyde (MDA) amount, together with BODIPY staining experiment, confirm that 6a and 6b can induce ferroptosis. Interestingly, in a nude mouse model, 6a showed a significant suppression of tumor growth with an inhibition rate of 63.4 %, without causing any weight loss of mice. The studies on the mechanism show that 6a causes immune cell death, increase the amount of TNF-α and IFN-γ, reduce IL-10 content, which further activates immune response to increase CD8⁺ T cells to prevent tumor growth. Therefore, 6a inhibits the tumor growth through stimulating the immune response to increase CD8⁺ T cells. In addition, the experiments in vitro show that the complexes through inhibition of PI3K/AKT/mTOR signaling pathway and intrinsic mitochondria pathway to cause cell apoptosis. These results demonstrate that Ru(II) complexes may be potent anticancer candidates for HepG2 tumor. Show less

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

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

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

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

Reactive molecules, including oxygen and nitrogen species, serve dual roles in human physiology. While they function as essential signaling molecules under normal physiological conditions, they contribute to cellular dysfunction and damage when produced in excess by normal metabolism or in response to stressors. Oxidative/nitrosative stress is a pathological state, resulting from the overproduction of reactive species exceeding the antioxidant capacity of the body, which is implicated in several chronic human diseases. Antioxidant Show less