Karl Ocius

RSC Chem Biol. 2025 May 30. doi: 10.1039/d5cb00086f. Online ahead of print.

ABSTRACT

Soluble peptidoglycan fragments produced by the gut bacteria are key effectors in microbiota-host crosstalk. Here, we biochemically characterized BbMep, an NlpC/p60 domain-containing peptidoglycan d,l-endopeptidase from Bifidobacterium bifidum, which efficiently digests Lys- or Orn-type sacculi. Digestion of human stool-derived muropeptides by BbMep enhances NOD2 activation.

PMID:40520142 | PMC:PMC12160582 | DOI:10.1039/d5cb00086f

Nat Microbiol. 2025 Jun 17. doi: 10.1038/s41564-025-02027-2. Online ahead of print.

ABSTRACT

Cyclic-di-AMP (c-di-AMP) is an essential second messenger in Bacillus subtilis and many other Gram-positive bacteria. Work over the past decade has revealed that this cyclic nucleotide controls cation and osmolyte transporters, leading to the hypothesis that c-di-AMP regulates cytoplasmic turgor pressure. Although the targets of c-di-AMP are well established, the signals that control the levels of this second messenger and the factors that transduce these signals are unknown. Here we report that c-di-AMP levels are modulated by the cyclase regulator CdaR in response to cell wall defects. We further demonstrate that changing the levels of c-di-AMP alters turgor pressure. Our data support a model in which CdaR senses defects in the cell wall and activates c-di-AMP synthesis in response. The increase in c-di-AMP reduces turgor, preventing lysis and enabling fortification of the peptidoglycan meshwork. Thus, a central function of c-di-AMP is to control cellular turgor in response to envelope defects.

PMID:40528006 | DOI:10.1038/s41564-025-02027-2

Chem Commun (Camb). 2025 Jun 9. doi: 10.1039/d5cc02577j. Online ahead of print.

ABSTRACT

This work identifies a novel antibacterial mechanism that targets the cell wall of the human pathogen Streptococcus pneumoniae. Unlike conventional cell-wall targeting antibiotics, which inhibit the natural cross-linking of peptidoglycan, we introduce artificial cross-links in the other main component of the Gram-positive cell wall, the teichoic acids, and show that it leads to impaired cell growth.

PMID:40485190 | DOI:10.1039/d5cc02577j

J Cancer Res Clin Oncol. 2025 May 24;151(5):174. doi: 10.1007/s00432-025-06227-5.

ABSTRACT

BACKGROUND: Histone deacetylases (HDAC) are involved in chromatin remodelling, and histone deacetylases inhibitors have become the interest of research and shown promising antitumor effects against various cancer.

METHODS: In the current study, an attempt was made to characterize the preclinical ADME properties of a novel hydroxamic based HDAC inhibitor, PAT-1102, with the help of in vitro assays and in vivo pharmacokinetic experiments in rats.

RESULTS: PAT-1102 showed high aqueous solubility and high Caco-2 permeability in the in vitro assays. It was found to be not a substrate of efflux protein P-gp, found stable in metabolism experiments with incubations of rat and human liver microsomes. Inhibition experiments of human recombinant CYP enzymes revealed that PAT-1102 was not considerably inhibited the major CYP enzymes. PAT-1102 exhibited low plasma protein binding of 58.1% and 54.5% in humans and rats, respectively. In vivo pharmacokinetic studies of PAT-1102 in male and female rats showed bioavailability of 3.7% and 3.0% by oral route, respectively. Previous research findings suggested that PAT-1102 is a potent pan-HDAC inhibitor with good preclinical efficacy.

CONCLUSION: Considering the overall ADME and pharmacokinetic profile of PAT-1102, as indicated by in vitro and in vivo experiments, the PAT-1102 could be considered as a potential candidate for the advancement of cancer therapy.

PMID:40411569 | PMC:PMC12103360 | DOI:10.1007/s00432-025-06227-5

Front Immunol. 2025 May 13;16:1546939. doi: 10.3389/fimmu.2025.1546939. eCollection 2025.

ABSTRACT

INTRODUCTION: Tumor immunotherapy has revolutionized cancer treatment, particularly through the use of immune checkpoint inhibitors targeting the PD-L1/PD-1 axis. While PD-L1 expression on tumor cells is an established predictive biomarker for therapeutic response, emerging evidence highlights the importance of PD-L1 expression on myeloid cells, both in the periphery and within the tumor microenvironment (TME). This study explores the immunomodulatory effects of the selective HDAC6 inhibitor ITF3756 on monocytes and dendritic cells (DCs).

METHODS: Monocytes were stimulated with the pro-inflammatory cytokine TNF-α and treated with ITF3756. PD-L1 and CD40 expression levels were assessed by flow cytometry. Transcriptomic and proteomic analyses were performed to characterize changes in gene and protein expression profiles. T cell proliferation was evaluated in co-culture assays. Additionally, the impact of ITF3756 was assessed in an in vivo murine model of colon cancer.

RESULTS: ITF3756 effectively downregulated PD-L1 expression in TNF-α-activated monocytes and enhanced their costimulatory capacity by increasing CD40 expression. Transcriptomic and proteomic analyses revealed that ITF3756 counteracted TNF-α pathway activation and downregulated multiple inhibitory immune checkpoint molecules, promoting a less immunosuppressive phenotype. In co-culture assays, ITF3756-treated monocytes and DCs significantly enhanced T cell proliferation. In vivo, ITF3756 treatment led to reduced tumor growth in a colon cancer model.

DISCUSSION: These findings demonstrate that selective HDAC6 inhibition by ITF3756 modulates myeloid cell functionality by diminishing inhibitory signals and promoting T cell activation. Thus, ITF3756 represents a promising immunomodulatory agent that could enhance the efficacy of immune checkpoint blockade in cancer immunotherapy.

PMID:40433358 | PMC:PMC12106391 | DOI:10.3389/fimmu.2025.1546939

Bioconjug Chem. 2025 May 21. doi: 10.1021/acs.bioconjchem.4c00575. Online ahead of print.

ABSTRACT

The strain-promoted alkyne-azide cycloaddition (SPAAC) reaction can be used to modify the surface of bacteria for a variety of applications including drug delivery, biosensing, and imaging. This is usually accomplished by first installing a small azide group within the peptidoglycan and then delivering exogenous cargo (e.g., a protein or nanoparticle) modified with a cyclooctyne group, such as dibenzocyclooctyne (DBCO), for in situ conjugation. However, DBCO is comparatively bulky and hydrophobic, increasing the propensity of some payloads to aggregate. In this study, we sought to invert this paradigm by exploring two novel strategies for incorporating DBCO into the peptidoglycan of Staphylococcus aureus and compared them to an established approach using DBCO-vancomycin. We demonstrate that DBCO-modified small molecules belonging to all three classes─a sortase peptide substrate (LPETG), two d-alanine derivatives, and vancomycin─can selectively label the S. aureus surface to varying degrees. In contrast to DBCO-vancomycin, the DBCO-d-alanine variants do not adversely affect the growth of S. aureus or lead to off-target labeling or toxicity in HEK293T or RAW 264.7 cells. Finally, we show that, unlike IgG3-Fc labeled with DBCO groups, IgG3-Fc labeled with azide groups is stable (i.e., remains water-soluble) under normal storage conditions, retains its ability to bind the immune receptor CD64, and can be successfully attached to the surface of DBCO-modified S. aureus. We believe that the labeling strategies explored herein will expand the paradigm of specific, nontoxic SPAAC-mediated labeling of the surface of S. aureus and other Gram-positive bacteria, opening the door for new applications using azide-modified cargo.

PMID:40398634 | DOI:10.1021/acs.bioconjchem.4c00575

Commun Biol. 2025 May 21;8(1):781. doi: 10.1038/s42003-025-08213-6.

ABSTRACT

Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) is a pattern recognition receptor of bacterial peptidoglycans. NOD1 facilitates the elimination of invading intracellular bacteria via autophagy induction. Here, we demonstrate that NOD1 exerts an anti-inflammatory effect mediated via the selective autophagy of host cell protein. In our study of Candida albicans water-soluble fraction (CAWS)-induced coronary arteritis, which is a mouse model of Kawasaki disease, we observed an exacerbated disease phenotype in NOD1-deficient mice. NOD1 deficiency induced a higher expression of inflammatory cytokines via CAWS and CAWS-induced endoplasmic reticulum (ER) stress in bone marrow-derived dendritic cells. Furthermore, exaggerated inflammation was dependent on apoptosis signal-regulated kinase 1 (ASK1). Notably, NOD1 directly interacted with ASK1, inducing selective autophagy of ASK1, which was dependent on ATG16L1, and thus competitively inhibiting ER stress-dependent ASK1 activation. Altogether, these results show that NOD1 modulates excessive inflammatory responses through the upregulation of autophagy.

PMID:40399666 | PMC:PMC12095521 | DOI:10.1038/s42003-025-08213-6

Acc Chem Res. 2025 May 21. doi: 10.1021/acs.accounts.5c00113. Online ahead of print.

ABSTRACT

ConspectusThe bacterial cell wall is a complex structure that is primarily composed of peptidoglycan (PG), which provides protection from the environment and structural rigidity for the cell. As such, PG plays an important role in bacterial survival, which has made its biosynthesis a crucial target for antibiotic development for many decades. Despite long-standing efforts to inhibit PG construction, much remains unknown about the enzymes required for PG biosynthesis or how PG composition and architecture are altered to enable adaptation to environmental stressors. This knowledge will be crucial in the identification of new ways to interfere with PG construction that could overcome widespread resistance to cell wall-targeting antibacterial agents.All bacterial species possess a suite of penicillin-binding proteins (PBPs), which are critical actors in PG construction and remodeling, as well as the main targets of β-lactam antibiotics. While the importance of the PBPs is well-known, the field lacks a complete understanding of PBP activity regulation, localization, and critical protein-protein interactions during the growth and division process. Bacteria possess between 4 and 16 PBP homologues with only one or several being genetically essential in each cell. A key outstanding question about these proteins is why bacteria expend the energy required to maintain this relatively large number of related proteins when so few are required to maintain life. The Carlson lab focuses on the development of chemical tools to address this fundamental question. In particular, we have generated a suite of chemical probes to selectively target one or a small number of PBP homologues in their catalytically active state. These activity-based probes (ABPs) have and will continue to enable a deeper understanding of the traits that differentiate the PBPs over the bacterial lifespan.In this account, we discuss the development of selective chemical tools to study the PBPs. Key to our success has been assessment of the PBP inhibition profiles of an expansive set of commercially available β-lactams in both Gram-positive and Gram-negative bacteria. This work has directly identified molecules that can be used in chemical genetic studies and provided scaffolds for the generation of PBP-selective ABPs. We also discovered a novel β-lactone scaffold that is exquisitely selective for PBPs over other protein classes and targets a different subclass of these proteins than related β-lactams. Using these probes, we have explored PG biosynthesis in Streptococcus pneumoniae, Escherichia coli and Bacillus subtilis yielding new insights about their cell wall construction and remodeling processes, as well as specialized activities under stress.

PMID:40396497 | DOI:10.1021/acs.accounts.5c00113