Brief Bioinform. 2025 May 1;26(3):bbaf269. doi: 10.1093/bib/bbaf269.

ABSTRACT

MOTIVATION: Signalling entropy measures the uncertainty or randomness in the signalling pathways of a biological system. It reflects the complexity and variability of protein interactions and can indicate how information is processed within cells. Higher signalling entropy often indicates a more dynamic and adaptive state, whereas lower entropy may imply a more stable and less responsive condition. Estimating signalling entropy has become a valuable method for studying and understanding the complexity of biological processes. This measure has the potential to shed valuable insights into various phenomena, including the mechanisms behind cell fate decisions, drug resistance, and disease progression. To examine the molecular changes within a system, signalling entropy is quantified through the integration of expression measurements and protein interaction networks. Experimental and computational issues, such as false positives and additional noise, can all compromise the accuracy of protein interaction networks. Correction methods can be used to mitigate spurious results, correct for experimental bias, and integrate data from multiple sources. However, to date, the effect of such approaches on entropy calculations, together with the impact of different underlying networks, has yet to be evaluated.

RESULTS: Here, we investigate how the topology of distinct protein interaction networks can alter the entropy calculation. We examine the entropy derived from different protein interaction networks. Additionally, we systematically evaluate different correction strategies, outlining their benefits and drawbacks along with identifying the most effective approaches for specific types of data and biological scenarios. This protocol outlines how to optimize the reliability of entropy calculations and ultimately leads to a deeper comprehension of biological processes and disease mechanisms.

PMID:40532109 | DOI:10.1093/bib/bbaf269

Sci Adv. 2025 Jun 20;11(25):eadt9936. doi: 10.1126/sciadv.adt9936. Epub 2025 Jun 18.

ABSTRACT

Paxillin (PXN) and focal adhesion kinase (FAK) are two major components of the focal adhesion complex, a multiprotein structure linking the intracellular cytoskeleton to the cell exterior. The interaction between the disordered amino-terminal domain of PXN and the carboxyl-terminal targeting domain of FAK (FAT) is necessary and sufficient for localizing FAK to focal adhesions. Furthermore, PXN serves as a platform for recruiting other proteins that together control the dynamic changes needed for cell migration and survival. Here, we show that the PXN N-domain undergoes significant compaction upon FAT binding, forming a 48-kilodalton multimodal complex with four major interconverting states. Although the complex is flexible, each state has unique sets of contacts involving disordered regions that are both highly represented in ensembles and conserved. PXN being a hub protein, the results provide a structural basis for understanding how shifts in the multistate equilibrium (e.g., through ligand binding and phosphorylation) may rewire cellular networks leading to phenotypic changes.

PMID:40532016 | DOI:10.1126/sciadv.adt9936

Sci Transl Med. 2025 Jun 18;17(803):eadr4058. doi: 10.1126/scitranslmed.adr4058. Epub 2025 Jun 18.

ABSTRACT

The treatment of solid tumors faces substantial hurdles because of inadequate drug delivery and the immunosuppressive tumor microenvironment. To address these challenges, we developed a therapeutic platform using macrophages loaded with ferritin-drug conjugates, referred to as macrophage-drug conjugates (MDC), and applied it to glioblastoma, an immunologically cold solid tumor. MDC loaded with ferritin-conjugated monomethyl auristatin E enabled efficient, cell contact-dependent transfer of the payload by a mechanism involving transfer of iron-binding proteins, from either mouse or human macrophages preferentially into glioma cells. This targeted delivery and therapeutic efficacy was demonstrated across in vitro coculture systems, ex vivo assays using dissociated glioblastoma patient tumor samples, and in vivo using orthotopic glioblastoma mouse models, all while maintaining a favorable preclinical safety profile evidenced by minimal systemic toxicity and localized drug biodistribution. Beyond direct tumor cell killing leading to significant tumor regression and prolonged survival in these models, MDC therapy reprogrammed the immunosuppressive tumor microenvironment. Immune profiling by spectral flow cytometry revealed enhanced infiltration and activation of cytotoxic T lymphocytes and B lymphocytes while reducing immunosuppressive regulatory T cells. This culminated in a robust, durable, T cell-dependent antitumor immune response, the necessity of which was confirmed through studies in immunodeficient mouse models and by lymphocyte depletion, and which conferred protection against tumor rechallenge. The combined cytotoxic and immunomodulatory effects highlight the potential of MDC therapy as a promising strategy for glioblastoma treatment and support its further clinical development.

PMID:40531966 | DOI:10.1126/scitranslmed.adr4058

J Med Chem. 2025 Jun 18. doi: 10.1021/acs.jmedchem.5c00348. Online ahead of print.

ABSTRACT

Fluorescent probes targeting proteins are used to investigate biological processes, requiring strong binding affinity and favorable fluorescence. In this study, we present the first fluostere with optimized fluorescence properties. We started exploring the fluorescence of acidic pyrazolo[1,5-a]pyridin-2-ol, and, by the introduction of EWGs, π-conjugation, incorporation of push-pull systems and rigid structures, we optimized emission profiles and QY, providing a first Structure-Fluorescence relationship (SFR) of the system. To provide proof of concept in biological applications, the established SFR was integrated with hDHODHi, an important oncology target, enabling the SAR designing fluorescent hDHODHi 11a and 14, with 11a being the most potent IC50 = 170 nM. These inhibitors were validated in vitro for their antileukemic and antiviral activity. As they are both environmentally sensitive fluorescent probes that can highlight their binding to the target, their fluorescence was found to colocalize in the mitochondria, where hDHODH is located, in cellular experiments.

PMID:40530899 | DOI:10.1021/acs.jmedchem.5c00348

Nucleic Acids Res. 2025 Jun 6;53(11):gkaf523. doi: 10.1093/nar/gkaf523.

ABSTRACT

Protein-RNA interactions underpin many critical biological processes, demanding the development of technologies to precisely characterize their nature and functions. Many such technologies depend upon cross-linking under mild irradiation conditions to stabilize contacts between amino acids and nucleobases; for example, the cross-linking of stable isotope labelled RNA coupled to mass spectrometry (CLIR-MS) method. A deeper understanding of the CLIR-MS workflow is required to maximize its impact for structural biology, particularly addressing the low abundance of cross-linking products and the information content of spatial/geometric restraints reflected by a cross-link. Here, we present a vastly improved CLIR-MS pipeline that features enhanced sample preparation, data acquisition and interpretation. These advances significantly increase the number of detected cross-link products per sample. We demonstrate that the procedure is robust against variation of key experimental parameters, including irradiation energy and temperature. Using this improved protocol on four protein-RNA complexes representing canonical and non-canonical RNA-binding domains, we propose for the first time the distances encoded by protein-RNA cross-links, enabling their use as structural restraints. We also compared the cross-linking of canonical RNA with 4-thiouracil-labeled counterparts, showing slight, but noticeable differences. The improved understanding of protein-RNA cross-links refines their structural interpretation and facilitates the adoption of the method in integrative/hybrid structural biology.

PMID:40530697 | DOI:10.1093/nar/gkaf523

Bioact Mater. 2025 Jun 5;52:92-122. doi: 10.1016/j.bioactmat.2025.05.030. eCollection 2025 Oct.

ABSTRACT

The emergence of novel viral pathogens and the limitations of conventional antiviral therapies necessitate innovative strategies to combat persistent and pandemic threats. This review details the role of viral infections and antiviral nanomedicines, delving into the mechanisms of action and antiviral advantages of nanomedicines, as well as the latest research advances in this field. The review systematically categorizes the mechanisms of antiviral nanodrugs into a framework that integrates previously fragmented knowledge, and innovatively summarizes the unique attributes and advantages of antiviral nanodrugs compared to small-molecule drugs. Nanotherapies are proposed in this review to conclude advanced nanoantivirals (e.g., light-activated nanophotosensitizers, biomimetic decoys, PROTAC-based degraders, and gene-silencing platforms) and offer a distinctive narrative perspective, with the aim of presenting a merged and integrated overview of nanodrugs. By intuitively highlighting their commonalities in mechanisms or similarities in application methods, readers may better appreciate the innovative characteristics of different antivirals. We further discuss translational challenges and propose interdisciplinary solutions and future directions to accelerate the development of next-generation antiviral strategies. This review aims to inspire transformative research at the nexus of virology, nanotechnology, and precision medicine.

PMID:40530413 | PMC:PMC12173073 | DOI:10.1016/j.bioactmat.2025.05.030

Oxid Med Cell Longev. 2025 Jun 10;2025:9782846. doi: 10.1155/omcl/9782846. eCollection 2025.

ABSTRACT

[This retracts the article DOI: 10.1155/2019/1707218.].

PMID:40530327 | PMC:PMC12173546 | DOI:10.1155/omcl/9782846

Metab Eng Commun. 2025 May 30;20:e00263. doi: 10.1016/j.mec.2025.e00263. eCollection 2025 Jun.

ABSTRACT

The plant hormone abscisic acid (ABA) has gained attention for its role in animals and humans, particularly due to its protective effects in various immune and inflammatory disorders. Given its high concentrations in fruits like figs, bilberries and apricots, ABA shows promise as a nutraceutical. However scalability, short half-life and cost limit the use of ABA-enriched fruit extracts and synthetic supplements. In this study, we propose an alternative ABA administration method to overcome these challenges. We genetically engineered a strain of the probiotic Saccharomyces boulardii to produce and deliver ABA directly to the gut of mice. Using the biosynthesis pathway from Botrytis cinerea, four genes (bcaba1-4) were integrated into S. boulardii, enabling ABA production at 30 °C, as previously described in Saccharomyces cerevisiae. Introducing an additional cytochrome P450 reductase gene resulted in a 7-fold increase in ABA titers, surpassing previous ABA-producing S. cerevisiae strains. Supplementation of the ABA-producing S. boulardii in the diet of mice (at a concentration of 5 × 108 CFU/g) led to effective gut colonization but resulted in low serum ABA levels (approximately 1.8 ng/mL). The absence of detectable serum ABA after administration of the ABA-producing probiotic through oral gavage, prompted further investigation to determine the underlying cause. The physiological body temperature (37 °C) was identified as a major bottleneck for ABA production. Modifications to enhance the mevalonate pathway flux improved ABA levels at 37 °C. However, additional modifications are needed to optimize ABA production before testing this probiotic in disease contexts in mice.

PMID:40530243 | PMC:PMC12173631 | DOI:10.1016/j.mec.2025.e00263

Mol Ther Oncol. 2025 Jun 4;33(2):200998. doi: 10.1016/j.omton.2025.200998. eCollection 2025 Jun 18.

NO ABSTRACT

PMID:40529619 | PMC:PMC12171805 | DOI:10.1016/j.omton.2025.200998

Front Microbiol. 2025 Jun 2;16:1570914. doi: 10.3389/fmicb.2025.1570914. eCollection 2025.

ABSTRACT

The consumption of traditional fermented foods and beverages plays an important role in the diet of Ethiopia, providing significant nutritional and health benefits to the local population. The present study aimed to investigate the microbial ecology and diversity of nine types of fermented products. These include two foods (Kotcho and Injera), one food condiment (Datta), and six beverages (Tej, Tella, Cheka, Kinito, Borde, and Shamita). A combination of metataxonomic and culturomic approaches was used to achieve a comprehensive characterization of the bacterial communities, together with a thorough physicochemical characterization of the fermented products. This study provides one of the most comprehensive microbial characterizations of a wide selection of Ethiopian fermented products, highlighting that some bacterial species involved in the fermentation processes could contribute to the safety and nutritional quality of fermented foods and, based on previous studies, could also play a key role in enhancing their potential probiotic properties.

PMID:40529576 | PMC:PMC12171217 | DOI:10.3389/fmicb.2025.1570914

RSC Chem Biol. 2025 Jun 12. doi: 10.1039/d5cb00082c. Online ahead of print.

ABSTRACT

Neuropeptides are critical endogenous signaling molecules involved in a wide range of biological processes, including neurotransmission, hormonal regulation, immune responses, and stress management. Despite their importance, the field of neuropeptide research has been historically hampered by significant technical challenges. These include their low abundance in biological systems, diverse and complex post-translational modifications, dynamic expression patterns, and susceptibility to degradation. As such, traditional proteomics approaches often fall short of accurately characterizing neuropeptides, underscoring the need for specialized methodologies to unlock their biological and translational potential. This review evaluates state-of-the-art quantitative mass spectrometry (MS)-based peptidomics, emphasizing their impact on neuropeptide analysis. We highlight how strategies in label-free and label-based quantitation, tandem MS acquisition, and mass spectrometry imaging provide unprecedented sensitivity and throughput for capturing the landscape of neuropeptides and their modifications. Importantly, the review bridges technological innovation with practical applications, highlighting how these approaches have been utilized to uncover novel neuropeptides and elucidate their roles in systems biology and disease pathways.

PMID:40529571 | PMC:PMC12168976 | DOI:10.1039/d5cb00082c

Front Genome Ed. 2025 Jun 3;7:1568072. doi: 10.3389/fgeed.2025.1568072. eCollection 2025.

ABSTRACT

Genome editing has presented enormous potential in the fields of medicine and agriculture. Here, we explore the social and regulatory aspects of genome editing from the perspective of food security. We provide recent examples of crop genome editing successes. We discuss the current regulatory framework for genome edited crops in North America and Europe, and present how public perception can influence international policies and trade.

PMID:40528898 | PMC:PMC12170646 | DOI:10.3389/fgeed.2025.1568072

Small. 2025 Jun 17:e2411476. doi: 10.1002/smll.202411476. Online ahead of print.

ABSTRACT

The United Nations have committed to end the epidemics of communicable diseases by 2030 (SDG Target 3.3). In contrast with this ambition, the rise of Multi Drug Resistant (MDR) and Pan Drug Resistant (PDR) bacteria poses a threat of a return to the pre-antibiotic era. It is of high priority to find new therapies that target the ESKAPEE group of pathogens and their drug-resistant strains. Antimicrobial peptides (AMPs) are an emerging class of antibiotics that hold promises of overcoming bacterial resistance by using both novel mechanisms of action as well as targeting already known pathways. The chemical space of AMPs is potentially huge and methodologies allowing the rational exploration of novel structures are highly needed. This review focuses on case studies that give novel insights about the mechanisms of action, resistance and selectivity of some relevant AMPs, exemplifying the importance of microscopic, computational and experimental tools. Particular focus will be devoted to bacterial membranes and how AMPs can target them while sparing human plasma membranes, in order to become safer drugs. The lessons learned from the literature cases give directions toward the development of AMPs as drug products.

PMID:40528540 | DOI:10.1002/smll.202411476

Curr Nutr Rep. 2025 Jun 18;14(1):81. doi: 10.1007/s13668-025-00671-y.

ABSTRACT

PURPOSE OF REVIEW: This review provides a comprehensive overview of iron metabolism, emphasizing the influence of dietary patterns-particularly vegetarian and vegan diets-on iron status and associated health outcomes.

RECENT FINDINGS: Concerns regarding iron deficiency anemia in individuals following plant-based diets necessitate a deeper comprehension of the factors affecting iron bioavailability and absorption. Non-heme iron, which is more abundant in plant-based sources, poses challenges about its lower bioavailability and this could contribute to an increased risk of anemia in these populations. However, recent studies challenge this assumption, revealing a more complex relationship between plant-based nutrition and iron status. Additionally, emerging evidence suggests that the potential association between red meat consumption and cancer may be partially mediated by the high intake of heme iron. This review highlights the complex dynamics of dietary iron in vegetarian and vegan diets, which, despite offering less bioavailable iron, often surpass the intake levels of omnivorous diets. The potential involvement of adaptive physiological mechanisms suggests variability in non-heme iron absorption to meet nutritional requirements. While well-planned plant-based diets can be nutritionally adequate, further research is needed to better understand their long-term effects on iron metabolism.

PMID:40528105 | DOI:10.1007/s13668-025-00671-y

Mol Syst Biol. 2025 Jun 17. doi: 10.1038/s44320-025-00119-z. Online ahead of print.

ABSTRACT

De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.

PMID:40527958 | DOI:10.1038/s44320-025-00119-z

NPJ Antimicrob Resist. 2025 Jun 17;3(1):56. doi: 10.1038/s44259-025-00121-3.

ABSTRACT

Herein, we report a library of 7-mer macrocyclic peptides designed by systematically replacing one, multiple, or all L-amino acids with their D-isomers in our previously identified hit compounds. Lead peptides, 15c and 16c, showed broad-spectrum activity against bacteria (Gram-positive minimum inhibitory activity (MIC 1.5-6.2 µg/mL and Gram-negative MIC 6.2-25 µg/mL) and fungi (MIC = 3.1-25 µg/mL). Additionally, peptides 15c and 16c showed rapid kill kinetics and biofilm degradation potential against both bacteria and fungi, while resistance development was not observed. The antimicrobial effect of these macrocyclic peptides was attributed to their membranolytic action, which was confirmed by calcein dye leakage assay and scanning electron microscopy analysis. Both peptides, 15c (HC50 = 335 µg/mL) and 16c (HC50 = 310 µg/mL), exhibited significantly lower hemolytic activity compared to their parent peptide p3 (HC50 = 230 µg/mL). At 100 µg/mL, both peptides showed >90% cell viability after 24 h incubation across four normal mammalian cell lines. Both peptides showed plasma stability (t1/2 ≥ 6 h), further supporting their therapeutic potential. Finally, the molecular mechanisms determining the pharmacological properties of a number of typical representatives of each series of synthesized peptides were investigated by NMR spectroscopy and computer simulations. The study revealed specific combinations of structural, dynamic, and hydrophobic parameters of these amphiphilic peptides that allow a reasonable prediction of their hemolytic activity. This Structure-Activity Relationship provides a basis for the rational design of peptides or peptidomimetics with predefined pharmacological profiles.

PMID:40527928 | DOI:10.1038/s44259-025-00121-3

Nat Commun. 2025 Jun 17;16(1):5296. doi: 10.1038/s41467-025-60525-7.

ABSTRACT

Due to low availability of CO2 in aquatic environment, microalgae have evolved a CO2 concentrating mechanism (CCM). It has long been thought that operation of CCM would suppress photorespiration by increasing the CO2 concentration at the Rubisco active site, but experimental evidence is scarce. To better explore the function of photorespiration in algae, we first characterized a Chlamydomonas reinhardtii mutant defected in low-CO2 inducible 20 (LCI20) and show that LCI20 is a chloroplast-envelope glutamate/malate transporter playing a role in photorespiration. By monitoring growth and glycolate excretion in mutants deficient in either CCM or photorespiration, we conclude that: (i.) CCM induction does not depend on photorespiration, (ii.) glycolate excretion together with glycolate dehydrogenase down-regulation prevents the toxic accumulation of non-metabolized photorespiratory metabolites, and (iii.) photorespiration is active at low CO2 when the CCM is operational. This work provides a foundation for a better understanding of the carbon cycle in the ocean where significant glycolate concentrations have been found.

PMID:40527898 | DOI:10.1038/s41467-025-60525-7

J Extracell Vesicles. 2025 Jun;14(6):e70094. doi: 10.1002/jev2.70094.

ABSTRACT

Extracellular vesicles (EVs) are mediators of intercellular communication through the transfer of nucleic acids, lipids and proteins between cells. This property makes bioengineered EVs promising therapeutic vectors. However, it remains challenging to isolate EVs with a therapeutic payload due to the heterogeneous nature of cargo loading into EVs. In this study, enrichment of EVs with a desired cargo was possible through engineering of the hallmark CD63 transmembrane protein. E-NoMi refers to engineered CD63 with mCherry on the inside of the EV membrane and a tag (3xFLAG) exposed on the outside of the EV membrane. To facilitate EV loading during biogenesis, cargo proteins, such as EGFP, Cre recombinase and the CRISPR-Cas nuclease (SaCas9), were fused to a nanobody (Nb) protein with a high affinity for mCherry. FLAG-tag-based immunocapture from cell conditioned media allowed selection of cargo-loaded E-NoMi-EVs, and tobacco etch virus (TEV) protease cleavage sites were used to remove the 3xFLAG-tag from the surface of E-NoMi-EVs after capture. For functional payload delivery to recipient cells, the vesicular stomatitis virus G (VSV-G) fusogenic protein was incorporated into E-NoMi-EVs to form fusogenic EV-based vectors (EVVs) and proved to be 10-fold more effective at cargo delivery than EVs generated by size-exclusion chromatography. Functional delivery of cargo with E-NoMi-EVVs was validated in two mouse brain models in vivo.

PMID:40527733 | DOI:10.1002/jev2.70094

Exp Neurol. 2025 Jun 15:115349. doi: 10.1016/j.expneurol.2025.115349. Online ahead of print.

ABSTRACT

The gut microbiota has emerged as a pivotal regulator of host inflammatory processes after traumatic brain injury (TBI). However, the mechanisms by which the gut microbiota communicates to the brain in TBI are still under investigation. We previously reported that gut microbiota depletion (GMD) using antibiotics after TBI resulted in increased microglial activation, reduced neurogenesis, and reduced T cell infiltration. In the present study, we have demonstrated that intestinal T cells contribute to the pool of cells infiltrating the brain after TBI. Depletion or genetic deletion of T cells before injury reversed GMD induced reductions in post-TBI neurogenesis. Short-chain fatty acid supplementation increased T regulatory and T helper1 cell infiltration to the brain along with restoring neurogenesis and microglia activation after TBI with GMD. These data suggest that T cell subsets are essential cellular mediators by which the gut microbiota modulates TBI pathogenesis, a finding with important therapeutic implications.

PMID:40527418 | DOI:10.1016/j.expneurol.2025.115349

Clin Immunol. 2025 Jun 15:110540. doi: 10.1016/j.clim.2025.110540. Online ahead of print.

ABSTRACT

Juvenile-onset systemic lupus erythematosus (jSLE) is a complex autoimmune/inflammatory disease in which genetic factors likely contribute to pathophysiology and clinical expression. This study explored associations between general (alternate allele counts; AAC) and gene-specific (alternate allele scores; GAAS) sequence variability, age at onset, sex, ancestry, disease activity/severity, organ involvement and treatments in jSLE. 289 participants from the UK JSLE Cohort Study underwent panel sequencing of 62 genes/genomic regions. Weighted AAC and GAAS were calculated. Correlation analyses and generalized linear models assessed associations between genetic burden, ancestry, age at diagnosis and clinical variables. AAC inversely correlated with age at diagnosis (R = -0.15, p = 0.01), primarily driven by South Asians (R = -0.28, p < 0.001). African/Caribbean patients exhibited higher AAC (p < 0.001). Clinical variables, including severity of renal involvement (ACP5, ITGAM, LYN, p < 0.001; TNFAIP3, p = 0.007), associated with GAAS. Genetic variability likely contributes to early disease expression and severity in jSLE, supporting patient stratification and personalised care.

PMID:40527401 | DOI:10.1016/j.clim.2025.110540