Karl Ocius

PLoS One. 2025 Nov 5;20(11):e0334632. doi: 10.1371/journal.pone.0334632. eCollection 2025.

ABSTRACT

Histone deacetylases (HDACs) mediate the removal of acetyl groups from lysine residues in both histone and non-histone proteins, and have been regarded as promising targets for drug discovery. As a central member of HDAC family, HDAC1 has been found to be closely linked to the occurrence and development of prostate cancer. In this study, we designed and synthesized a new series of 3-phenylisoxazole HDAC1 inhibitors based on the hit 7, identified by in-house compound library screening. The structure-activity relationship studies (SARs) indicated that the R1 position was relatively tolerated for activity. The linker length at R2 exerted a significant influence on activity with the relative orders of butyl > propyl > ethyl > methyl. Among synthetic 16 compounds, compound 17 indicated the strongest HDAC1 inhibitory effect with the inhibition rate of 86.78% at the concentration of 1000 nM. In addition, derivative 17 could not only well occupy the active pocket of HDAC1, but also showed favorable drug-like properties. More importantly, molecule 17 exerted potent anti-proliferative activity on prostate cancer PC3 cells with the IC50 value of 5.82 μM, and had no significant toxicity against normal prostate WPMY-1 cells. Collectively, these findings validate phenylisoxazole derivative 17 as a promising lead compound for further optimization and development.

PMID:41191566 | PMC:PMC12588503 | DOI:10.1371/journal.pone.0334632

Proc Natl Acad Sci U S A. 2025 Nov 11;122(45):e2514198122. doi: 10.1073/pnas.2514198122. Epub 2025 Nov 3.

ABSTRACT

The peptidoglycan (PG) cell wall is critical for bacterial growth and survival and is a primary antibiotic target. MreD is an essential accessory factor of the Rod complex, which carries out PG synthesis during elongation, yet little is known about how MreD facilitates this process. Here, we present the cryoelectron microscopy structure of Thermus thermophilus MreD in complex with another essential Rod complex component, MreC. The structure reveals that a periplasmic-facing pocket of MreD interacts with multiple membrane-proximal regions of MreC. We use single-molecule FRET to show that MreD controls the conformation of MreC through these contacts, inducing a state primed for Rod complex activation. Using Escherichia coli as a model, we demonstrate that disrupting these interactions abolishes Rod complex activity in vivo. Our findings reveal the role of MreD in bacterial cell shape determination and highlight its potential as an antibiotic target.

PMID:41183199 | DOI:10.1073/pnas.2514198122

Chembiochem. 2025 Dec 11;26(24):e202500629. doi: 10.1002/cbic.202500629. Epub 2025 Nov 2.

ABSTRACT

In this work, we develop a platform for multimerizing peptides/miniproteins using various polyvalent thioester cores derived from easy-to-synthesize N-hydroxysuccinimide esters. We employed native chemical ligation to attach multiple copies of peptide/miniprotein around a fixed multi-armed thioester core in a one-pot fashion, leading to the first-generation multimers. Further, using a reverse thioether ligation strategy, we synthesized second-generation branched homo/hetero multimers. The reactions proceed under an aqueous environment that closely mimics physiological conditions, forming multimeric products with yields ranging from 30% to 90%. The general utility of this strategy is showcased by the synthesis of multimeric linear and bicyclic peptides, bicyclic peptide-cell penetrating peptide conjugates, and multimeric miniproteins which show picomolar affinity against SARS-CoV-2 receptor binding domain. We believe that this modular approach of generating multimeric molecules should find broad applicability in peptide chemistry and chemical biology.

PMID:41176651 | DOI:10.1002/cbic.202500629

Biology (Basel). 2025 Oct 14;14(10):1414. doi: 10.3390/biology14101414.

ABSTRACT

Mycobacterium tuberculosis (M. tuberculosis) has developed some strategies to evade host immune responses through ubiquitination, thereby facilitating persistent mycobacterial infection. The Rv3717 protein has been identified as a peptidoglycan (PG) amidase that contributes to mycobacterial survival, but its exact mechanism is still unclear. The findings of this study indicate that Rv3717 inhibits mycobacterial clearance within pulmonary epithelial cells. To elucidate the molecular mechanisms by which Rv3717 facilitates persistent infection, we identified intracellular candidates interacting with Rv3717 using co-immunoprecipitation (Co-IP) combined with liquid chromatography-mass spectrometry (LC-MS/MS). The unique proteins are categorized into three functional networks: mRNA splicing, the immune system process, and the translation process through Protein-Protein Interaction (PPI) analysis. The candidate interacting proteins of Rv3717 are involved in interleukin-2 enhancer-binding factor 2 (ILF2) and TAF15, as well as the polyubiquitin chain (UBC) and E3 ubiquitin ligase TRIM21. Our results suggest that intracellular Rv3717 is likely to influence biological processes through the potential interacting proteins. Our findings confirmed that Rv3717 interacted with interleukin enhancer-binding factor 2 (ILF2) through Co-IP and immunofluorescence assays. Furthermore, Rv3717 was verified to bind with ubiquitin and be degraded through the proteasome system. More importantly, the ubiquitination of Rv3717 accelerated the proteasomal degradation of ILF2 and downregulated the expression of IL-2. This study is the first to propose that the ubiquitination of the mycobacterial membrane vesicle-associated protein Rv3717 facilitates the proteasomal degradation of ILF2, resulting in the downregulation of IL-2 expression. Overall, the role of intracellular Rv3717 in promoting mycobacterial survival is associated with its ubiquitination and the proteasomal degradation of ILF2.

PMID:41154817 | PMC:PMC12561918 | DOI:10.3390/biology14101414

JACS Au. 2025 Oct 1;5(10):4893-4903. doi: 10.1021/jacsau.5c00832. eCollection 2025 Oct 27.

ABSTRACT

The inverse electron demand Diels-Alder (IEDDA) click reaction of tetrazine (Tz) with trans-cyclooctene (TCO), which takes place at an exceptionally high rate, has excellent orthogonality and biocompatibility. As a result, the unrivaled capacity of this process enables it to serve as a viable chemical tool for protein modification even in humans. However, the utility of this click reaction is impeded by the limited number of practical methods for the incorporation of the Tz moiety into proteins. Herein, we describe the simple dual-functional Tz-substituted allyl acetate reagent, TzAA, that targets bis-thiol moieties for direct, site-selective installation of a Tz group into native peptides and proteins. In addition to functioning as an IEDDA-based click reaction center, the Tz moiety in TzAA activates double Michael cascade reactions of the allylic acetate moiety with bis-thiols or from disulfide derivatives. We demonstrated the versatility and generality of bioconjugation reactions of TzAA that produce well-defined peptide and protein conjugates without compromising biological activities. The Tz-conjugates serve as a versatile handle for facile click reactions to introduce various functionalities. Moreover, the reagent is validated as a versatile linker for the synthesis of stapled peptides with protecting-group-free peptides. As shown, the Tz-derived cyclic peptides offer unrivaled capacity for selective targeting and delivery of TCO-caged prodrugs with reduced side effects. Collectively, the results of this investigation demonstrate that the probe with its unrivaled dual bioconjugation and click capacity, operational simplicity, and high labeling efficiency will offer a powerful chemical tool for direct, site-selective peptide/protein modification.

PMID:41169594 | PMC:PMC12569695 | DOI:10.1021/jacsau.5c00832

Adv Sci (Weinh). 2025 Oct 27:e14408. doi: 10.1002/advs.202514408. Online ahead of print.

ABSTRACT

Lysozymes are well-known for their ability to cleave bacterial peptidoglycan, but their potential to hydrolyze viral components as a form of antiviral defense remains poorly understood. This study demonstrates that insect i-type lysozymes (Lyz-I1), regulated by the Toll signaling pathway, function as proteases that directly cleave viral proteins. Structural and functional analyses reveal that the catalytic dyad Glu34/Asp50 in leafhopper Lyz-I1, while retaining its essential role in bacterial peptidoglycan hydrolysis, also mediates specific binding to Lys180 on the viroplasm protein Pns9 of rice gall dwarf virus (RGDV). This interaction catalyzes the cleavage of the adjacent peptide bond of Lys180, leading to Pns9 degradation, which disrupts viroplasm assembly and inhibits viral replication. Notably, this proteolytic antiviral mechanism of Lyz-I1 shows evolutionary conservation across major rice reoviruses and their respective leafhopper or planthopper vectors. Additionally, leafhopper Lyz-I1 undergoes liquid-liquid phase separation, forming biomolecular condensates that concentrate Pns9 and enhance proteolytic efficiency. Critically, exogenous application of Lyz-I1 not only effectively reduces viral titer and disease symptoms in RGDV-infected rice plants but also induces plant immune defense. Consequently, this work provides the evidence that lysozymes can function as specific antiviral proteases, establishing a foundation for innovative control strategies against viral diseases.

PMID:41144906 | DOI:10.1002/advs.202514408