Karl Ocius

Nature Chemical Biology, Published online: 06 April 2026; doi:10.1038/s41589-026-02181-6

Endosomal Toll-like receptors (TLRs) are central to the innate immune response but their overactivation can cause systemic inflammation and disease. Now, new small molecules targeting the interaction between Munc13-4 and syntaxin 7 essential for endosomal maturation impair overactivation of endosomal TLR-dependent pathways and inflammation.

Nature Immunology, Published online: 01 April 2026; doi:10.1038/s41590-026-02499-2

Pyruvate-mediated PTM

Nature Microbiology, Published online: 03 April 2026; doi:10.1038/s41564-026-02317-3

Spatial transcriptomics and immunofluorescence microscopy of human samples and mouse models reveal that infection-driven cholesterol overload in granulomas impairs macrophage–CD4+ T cell interactions and anti-tuberculosis immunity.

A proximity-induced, mass-encoded activity-based protein profiling (ABPP) approach transfers a MALDI-detectable α-cyano-4-hydroxycinnamic acid (CHCA) tag directly to active proteases. This tag enables the direct, multiplexed, and quantitative detection of enzyme activity in complex proteomes without enrichment or purification.

ABSTRACT

Conventional activity-based probes in activity-based protein profiling (ABPP) require enrichment or reporter tags for detection, which limits sensitivity and multiplexing. Here, we present an enrichment-free chemoproteomic approach that enables direct mass spectrometric detection by Matrix-Assisted Laser Desorption/Ionization (MALDI) of active proteases. An active-site–directed affinity probe transfers, through a proximity-induced reaction, a MALDI-detectable α-cyano-4-hydroxycinnamic acid (CHCA) tag exclusively to catalytically active forms of matrix metalloproteases (MMPs). The CHCA label enhances ionization efficiency and markedly improves signal-to-noise ratios, allowing confident identification of CHCA-labelled peptides under discriminating analytical conditions. Each active metalloprotease is thereby, associated with a distinct set of CHCA signature peptides, defining its activity fingerprint. This workflow achieves multiplexed and quantitative activity profiling of MMPs, directly in complex proteomes. This design expands ABPP into the mass spectrometry domain and establishes a robust platform for activity-based enzyme detection.

Proceedings of the National Academy of Sciences, Volume 123, Issue 14, April 2026.
SignificanceOpportunistic infections caused byPseudomonas aeruginosa(Pa) pose serious risks to immunocompromised patients and complicate care across modern medicine—from cancer treatment to surgery and intensive care. We found that a clinically relevant,...

Synthetic fluorescence resonance energy transfer (FRET)-based fluorogenic probes report on esterases that hydrolyze arabinogalactan mycolate (AGM) glycolipids, which form the foundation of the mycobacterial outer membrane. Mycomembrane-degrading hydrolases, such as the mycobacteriophage enzyme LysB, are of interest due to their involvement in cell envelope remodeling and their potential as therapeutic agents against Mycobacterium tuberculosis and related pathogens.

Mycobacteria, including the tuberculosis pathogen Mycobacterium tuberculosis, are enclosed by a highly complex cell envelope with an outer membrane, or mycomembrane, which provides extraordinary protection from antibiotics and other stresses. The inner leaflet of the mycomembrane consists of arabinogalactan-linked mycolate (AGM), which is an enormous glycoconjugate comprising mycolic acids esterified to terminal D-arabinofuranosyl residues of an underlying arabinogalactan–peptidoglycan complex, also referred to as the mycoloyl-arabinogalactan–peptidoglycan (mAGP) complex. Whereas AGM biosynthesis is comparatively well characterized, less is known about AGM degradation by endogenous or exogenous factors. To facilitate studies on AGM breakdown by hydrolytic enzymes, here we synthesized fluorescence resonance energy transfer (FRET)-based mono- and disaccharide probes that mimic fragments of AGM and are designed to fluoresce upon cleavage. We devised a synthetic route that established the glycolipid core with the desired regio- and stereochemistry and allowed late-stage selective functionalization of the core with a FRET pair. Our data show that the intact FRET-AGM probes exist in a fluorescence-quenched state, but when exposed to lysin B (LysB), an AGM-degrading mycobacteriophage hydrolase with therapeutic relevance, the probes were activated through lipid ester hydrolysis, thereby generating fluorescence signal. FRET-AGM probes were activated by known mycomembrane glycolipid hydrolases, but not by several other types of hydrolases, demonstrating specificity. FRET-AGM probes may be useful in the future for identifying novel AGM hydrolases and quantitatively monitoring the activity of AGM hydrolases, which could provide insights into mycomembrane degradative processes and aid in tuberculosis therapeutic development.

Efficient intracellular delivery of proteins constitutes an indispensable component in a diversity of fundamental research applications but remains challenging due to their entrapment in the endosome. We now report that benzaldehyde-tagged cationic cell-penetrating peptides are highly effective in accessing cytosol in an energy-independent manner via dynamic imine anchoring, enabling the intracellular delivery of the attached bioactive cargos.

ABSTRACT

Cytosolic delivery of biomacromolecules constitutes an indispensable component in cell therapies, genome editing, and a diversity of fundamental research applications but remains challenging. Delivery by cell-penetrating peptides (CPPs) has been extensively investigated, especially owing to their advantages in minimal cytotoxicity and low transcriptional interference. However, for the vast majority of CPPs, cellular entry occurs predominantly via endocytic uptake, leading to endosomal entrapment and cargo degradation. Herein, we demonstrate that benzaldehyde-tagged cationic CPPs are highly effective in accessing the cytosol of different human cell lines in an energy-independent manner even at low micromolar concentrations. Live-cell reductive amination coupled with membrane fractionation and fluorescence imaging confirms imine-mediated covalent interaction between benzaldehyde-tagged CPP and native membrane proteins. Comparative interactors profiling using CPP-based photo-crosslinking probes further identifies cell membrane partners for CPPs and reveals a spatial interaction network consistent with the observed subcellular distributions. Furthermore, benzaldehyde-tagged CPPs form more stable delivery complexes with protein cargos via transient imine bonds and other non-covalent interactions. Finally, we showcase the efficient delivery of diverse bioactive proteins and peptides into the cytosol of various cell lines, enabling apoptosis induction or actin filament staining. This imine anchoring technique would open up new avenues for CPPs-based intracellular delivery of biomacromolecules.

Nature Immunology, Published online: 24 March 2026; doi:10.1038/s41590-026-02480-z

Here, the authors suggest that, when major histocompatibility complex class I is downregulated on allogenic or tumor cells, they are more susceptible to CD4+ T cell-mediated ferroptosis.

Nature Communications, Published online: 26 March 2026; doi:10.1038/s41467-026-71093-9

This work develops DJX-A-KM, a small-molecule KRASG12C degrader that recruits E3 ligase FBXO28 via dual covalent binding, inducing potent degradation. This strategy can possibly be extended to pan-KRAS degraders against a broader spectrum of KRAS mutations.

Zhuang et al. address limited antibody-drug conjugates (ADCs) internalization by developing ubitaADCs that harness receptor ubiquitination. By engaging membrane E3 ligases, ubitaADCs promote receptor endocytosis and lysosomal trafficking, enhancing intracellular payload delivery and supporting a modular strategy applicable to multiple tumor-associated receptors.

Nature Chemical Biology, Published online: 25 March 2026; doi:10.1038/s41589-026-02169-2

Song et al. find that biomolecular condensates can catalyze reductive amination of metabolites through a nonenzymatic mechanism, mediating C–N bond formation in vitro and impacting cellular metabolism in Escherichia coli.

Here’s the other cognition/aging/Alzheimer’s paper that caught my eye. In a similar way to the work I highlighted yesterday on proteins released by the liver affecting the blood-brain barrier and overall brain function, this one is finding another external signal, from from an unexpected direction.

The authors studied the intestinal microbiomes of mice as they aged, and found that species that produce medium-chain fatty acids become more and more prevalent. Then a complex series of events start taking place: these metabolites are ligands for the human GPR84 protein and can drive inflammation in myeloid cells through that activation. This in turn weakens the neural traffic through the vagal system, and this loss of “interoceptive” signaling to the brain leads to a decline in hippocampal function. Impaired memory, in other words. 

Now that’s one that I wouldn’t have seen coming, but as the paper shows in its references, there are a number of other reports pointing in this microbiome/memory direction. Now overall, the signal/noise of microbiome work is not as high as it should be, but papers like this new one are an important step in shoring up such hypotheses, trying to bridge some of the “by some mechanism that we haven’t figured out yet” gaps. It’s not that new and interesting ideas have to eliminate all of those leaps, but if you have to invoke that sort of thing too many times you’re asking for trouble. Here’s how you avoid that (hint: it involves an awful lot of work).

One experiment done here was to house very young (two-month old) mice with old (18-month-old) ones, which led to exchange of microbiome species between the two cohorts and an equilibrium that looked quite a bit more like the old ones. This didn’t seem to have any real effects on physical health and energy levels (or even things like exploratory behavior), but the short-term and long-term memory task performance of the young mice declined. To control for social effects, the team tried things like direct faecal microbiome transplants from the old mice into the young ones, and this recapitulated the memory effects all by itself. Meanwhile, co-housing gnotobiotic (germ-free) mice of both age groups did not affect the memories of the younger ones. Similarly, treating regular groups of young and old mice with two weeks of antibiotics also restored memory task performance in both cohorts.

And yes, the aged germ-free mice also performed much better on memory tests than the ones with typical microbiomes, so all of these results point in the same direction. There appears to be a gut microbial factor that impairs memory in older mice. Looking at the bacterial species that were present across different ages, Parabacteroides goldsteinii looked like the top candidate. (That one has already been the subject of a great deal of microbiome work in humans, as that link will show) Colonizing either germ-free or post-antibiotic mice with this species alone brought on the memory trouble, but this effect could not be demonstrated with other species that increased with age, nor with some that showed no real change as the mice aged.

Looking at the brains of the impaired mice, it appeared that neuronal function was disrupted in the hippocampus and in several areas known to be involved with sensory processing. A weird and interesting result was that many of the neurons involved in the vagus nerve’s gut-to-brain connections express the TRPV1 vanilloid receptor. Chemogenetic silencing of this receptor gave memory behavior similar to the aged mice, while activation of it seemed to restore function in the elderly cohort. That extended even to such low-tech methods as giving the mice capsaicin as a TRPV1 agonist (!) Other gut-responsive signals such as CCK or GLP-1 showed improvements in the presence of added agonists, although their underlying levels were not changed with aging and/or P. goldsteinii infection.

Further experiments showed that (as mentioned above) medium-chain fatty acids produced by those bacteria seem to be the actual signal driving these effects. Oral administration of things like decanoic acid and 3-hydroxyoctanoic acid were enough to affect cognition by themselves, and demonstrated effects along the whole causal chain the above work had laid out (vagus nerve activation and the sensory and hippocampal brain regions). These are known to be ligands for GPR84, and the team showed that mice with inactivating mutations in that receptor were immune to the effects of added medium-chain acids and showed delayed onset of memory trouble in general as compared to wild-type mice. The receptor is largely found in myeloid cells (macrophages, monocytes, and neutrophils) and ablating these also restored memory function (demonstrated through a set of bone-marrow experiments).

This looks to me like a very solid paper where the authors have tried to shore up every step of their hypothesis. Inflammation-driven defects in interoceptive signaling truly does look like a cause of memory decline in mice: but does it work that way in humans? You can bet that work is going on as we speak to find that out, but this pathway fits in very well with the overall idea that inappropriate inflammation is a driver of age-related brain dysfunction. But I have to say, we weren’t looking for it first in the gut rather than directly in the brain! There’s clearly a lot of work to be done here, and direct pharmacological intervention in these interoceptive pathways could really be beneficial. Starting with more hot sauce, given those capsaicin results? Try it today!