ACS Bio & Med Chem Au最新文献

F₄₂₀-dependent glucose-6-phosphate dehydrogenase (FGD) catalyzes the oxidation of glucose-6-phosphate (G6P) to 6-phosphogluconolactone (6PG). Recent phylogenetic analyses have identified a new subclass of these enzymes, F₄₂₀-dependent sugar-6-phosphate dehydrogenases (FSDs), which act on a broader range of 6-phosphate sugars, including fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P). One such enzyme from Cryptosporangium arvum (Cryar-FGD) was characterized by using binding assays and kinetic analyses, nuclear magnetic resonance (NMR), and mass spectrometry. Results showed strong binding affinities for all substrates. Steady-state kinetic analysis revealed that G6P has the highest catalytic efficiency, with a k_cat(app) of 6.4 ± 0.2 s^–1, compared to 1.4 ± 0.1 s^–1 for F6P and 0.32 ± 0.02 s^–1 for M6P. Pre steady-state spectral features for the G6P reaction resembled those of Mycobacterium tuberculosis FGD. While the F6P reaction displayed distinct spectral features, F₄₂₀ reduction was still observed. In contrast, the spectra for the M6P reaction were markedly different from those of G6P and F6P. Across all substrates, no catalytic intermediates were detected, and hydride transfer was not rate-limiting. As with G6P, the reaction with F6P also produced 6PG. Notably, NMR data showed that F6P was isomerized to G6P, suggesting isomerase activity. In contrast, M6P induced only spectral shifts with no evidence of isomerization or 6PG formation. However, mass spectrometry confirmed oxidized products for all three sugars, each with a mass of 299.0 ± 0.1. Collectively, these findings reveal that Cryar-FGD exhibits both dehydrogenase and isomerase activity, uncovering a newly identified dual enzymatic function and establishing its role as a multifunctional enzyme.

RNA biology exemplifies functional heterogeneity─distinct RNA classes are expressed in tissue- and development-specific contexts, adopt dynamic conformational ensembles, and form intricate, context-dependent interactions with proteins and other molecules to regulate gene expression. These features make RNA a powerful metaphor for reimagining scientific culture. Just as RNA achieves biological complexity through versatility, feedback loops, and communication, research environments thrive when they support dynamic interactions, structural adaptability, and the intentional inclusion of divergent perspectives and experiences. However, unlike RNA, research culture is shaped by human behavior, institutional norms, and systemic barriers─forces that can suppress innovation and limit who contributes to scientific discovery. Scientific excellence demands the integration of wide-ranging perspectives to challenge paradigms and push boundaries. Yet entrenched structures often reward conformity and marginalize creativity born from difference. By embracing the principles inherent to RNA biology─contextual responsiveness, structural plasticity, and cooperativity─we can transform scientific culture into one that is more inclusive, welcoming, and adaptable. This perspective argues that the biological elegance of RNA offers more than molecular insight; it provides a conceptual framework for building research environments that harness the full spectrum of talent in our richly heterogeneous society, ultimately accelerating scientific progress and broadening its societal impact.

Sequence motifs or patterns found in natural antimicrobial peptides (AMPs) have a great impact on their microbicidal activities. Here, through database inquiries and biological assays, we explore the enhanced antibacterial function associated with poly arginine (poly-R) motifs that typically occur as 3–5 concatenated R residues in many natural AMPs. Using a suite of biophysical techniques, we explore the structural consequences of a C-terminal poly-R motif at membranes and correlate our findings with the functional assays. We use natural peptides, such as Tilapia piscidin 4 (TP4), as an example of how various segments in an AMP play separate and synergistic roles to achieve unmatched bactericidal effects. The function of the poly-R segment is highly consequential since the simple addition of a five-arginine (R5) tail to an otherwise inert and weakly binding helical peptide creates a potent AMP. We investigate interactions of AMPs with lipid bilayers mimicking bacterial membrane compositions, including lipopolysaccharides, to show that the poly-R tail has a key role in initiating membrane destabilization through lipid segregation and water sequestration effects, all of which facilitate insertion and translocation of the amphipathic, α-helical N-terminal segment through the membrane. We compiled a large set of natural AMP sequences and MIC values to show that, statistically, the poly-R sequence motifs have, in average, a greater impact on the overall antimicrobial efficacy than equivalent sequences with poly-K motifs and similar charge densities. We discuss our observations in light of the unique structural and hydration properties of arginine residues.

Alzheimer’s disease (AD) and AD-related dementias (ADRD) represent a significant health challenge, with a growing impact on marginalized populations who often experience inequities in overall healthcare access and outcomes. Many factors contribute to these inequalities and can impact the benefits of broad appreciation of new technologies in AD/ADRD to these populations. For example, clinical proteomics offers a promising avenue for early and timely detection of disease and elucidation of the mechanisms of AD/ADRD. Unfortunately, gaps exist in the access and application of proteomic innovations for the health of marginalized communities. This editorial (1) highlights systemic barriers and explores the underlying factors that contribute to these inequities, (2) examines health disparities in the implementation of clinical proteomics tools for the management of AD/ADRD among marginalized populations, and (3) offers opportunities for advancing clinical proteomics in AD/ADRD. Implementation by basic and clinical researchers will lead to a more effective and inclusive approach to combatting AD/ADRD disparities.

The prevalence of fungal infections and contamination has increased alarmingly over the past decade, posing a significant threat to human health and the food supply and negatively affecting welfare. This escalating concern is primarily attributed to the lack of safe, effective, and widely available antifungal agents; the increasing spread of (multi)drug resistance to conventional antifungal treatments; and substantial epidemiological shifts in fungal pathogens. Decision-making bodies have recognized the urgency of this situation and prioritized efforts to address and mitigate the spread of drug-resistant fungal infections by developing and implementing innovative antifungal strategies, including using drug combinations, designing fundamentally new antifungal compounds with fungus-specific mechanisms of action and a minimal risk of resistance development, drug repurposing, and exploring alternative approaches, such as biomolecules, nanotechnology, and biological control. This review aims to provide a comprehensive overview of the current challenges associated with fungal infections in medicine and agriculture as well as the latest advancements and potential solutions.

Caspases are a family of cysteine proteases that act as molecular scissors to cleave substrates and regulate biological processes, such as programmed cell death and inflammation. Extensive efforts have been made to identify caspase substrates and to determine the factors that dictate specificity. We recently discovered that human inflammatory caspases (caspases-1, -4, and -5) cleave the cytokines IL-1β and IL-18 in a sequence-dependent manner. Here, we report the development of a new peptide-based probe and inhibitor derived from the tetrapeptide sequence of IL-18 (LESD). The LESD-based inhibitor showed a strong preference for caspase-8 with an IC₅₀ of 50 nM, and was more potent in vitro than the commonly used zIETD-FMK inhibitor, which is considered the most selective and potent caspase-8 inhibitor. We further demonstrated that the LESD-based inhibitor prevents caspase-8 activation during Yersinia pseudotuberculosis infection in primary bone marrow-derived macrophages. In addition, we systematically characterized the selectivity and potency of known substrates and inhibitors of the apoptotic and inflammatory caspases using standardized activity units of each caspase. Our findings reveal that VX-765, a known inhibitor of caspases-1 and -4, also inhibits caspase-8 (IC₅₀ = 1 μM). Even when specificities are shared, the caspases exhibit different efficiencies and potencies for shared substrates and inhibitors. Altogether, we report the development of new tools that will facilitate the study of caspases and their roles in biology.

N-acyl ethanolamines represent conserved lipophilic signaling molecules that function as endogenous ligands at G-protein-coupled receptors, ion channels, and nuclear receptors. Using a combination of comparative ultrahigh-performance liquid chromatography electrospray ionization high-resolution tandem mass spectrometry (UHPLC-ESI-HR-MS^E) analysis and microreactions, a diversity of glycosylated N-acyl phosphoethanolamines were characterized in Caenorhabditis nematodes. Representative examples were enriched by RP-C18 chromatography and identified by NMR spectroscopy. Comparative metabolomics and isotope incorporation experiments revealed that the biosynthesis of the homologous N-acyl building blocks (approximately 50 compounds) depends on the bacterial food source, chain elongation and desaturation of food-derived fatty acids, or their de novo biosynthesis by the nematode, whereas the biosynthesis of medium-chain N-acyl units depends on the peroxisomal β-oxidation cycle via the 3-ketoacyl-S-CoA thiolase daf-22. Glycosylation of these lipophilic N-acyl ethanolamines results in amphiphilic modular metabolites (approximately 100 identified compounds) that are released into the environment and exhibit potential signaling functions. Exclusively male-produced β-sophorosyl N-acyl-phosphoethanolamines like SNAP-13:1cyclo retain females of Caenorhabditis wallacei and Caenorhabditis brenneri, and its biosynthesis requires bacterial cyclo fatty acids 17:1cyclo and 19:1cyclo, thereby translating growth phase-dependent bacterial lipogeneses into a behavioral signal. Amphiphilic 2-(β-glucosyl)-glyceryl N-eicosapentaenoyl phosphoethanolamine (GGp-NAE-20:5), a dominating component of the Caenorhabditis elegans metabolome, represents a water-soluble derivative of N-eicosapentaenoyl ethanolamine (NAE 20:5), potentially enabling intra- and interspecies endocannabinoid signaling.

N⁶-Adenosine methylation is the most abundant modification of mRNA. The three members of the YTH domain family proteins (YTHDF1–3) recognize in the cytoplasm the m⁶A-RNA modification. We screened a library of about 500,000 fragments (i.e., molecules with 11–20 non-hydrogen atoms) by docking into YTHDF2, which resulted in the identification of six active compounds among 47 tested in vitro (hit rate of 13%). The acquisition of 28 analogues of the docking hits provided an additional set of 10 active compounds (IC₅₀ < 100 μM). Protein crystallography-guided optimization of a ligand-efficient fragment by the synthesis of 32 derivatives culminated in a series of YTHDF2 ligands, which show low-micromolar affinity measured by a fluorescence polarization (FP) assay and a homogeneous time-resolved fluorescence-based (HTRF) assay. The series is characterized by very favorable ligand efficiency (of about 0.3–0.4 kcal/mol per non-hydrogen atom). Compound 23 binds to YTHDF2 according to the FP and HTRF assays with a K_d value of 1.3 μM and an IC₅₀ value of 11 μM, respectively, and it is selective against all of the other YTH reader proteins. Several compounds of the series bind to the three YTHDF proteins with similar low-micromolar affinity, while they are less potent for YTHDC1 and YTHDC2. In contrast, compounds 17 and 30 bind also to YTHDC2, with K_d of 6.3 and 4.9 μM, respectively. We also disclose six crystal structures of YTHDF2 in the complex with the fragments identified by docking.