Rachita Dash

Antimicrob Agents Chemother. 2025 Feb 13;69(2):e0117424. doi: 10.1128/aac.01174-24. Epub 2024 Dec 23.

ABSTRACT

Mycobacterium abscessus (Mab) presents significant clinical challenges. This study evaluated the synergistic effects of a β-lactam and β-lactamase inhibitor combination against Mab and explored the underlying mechanisms. Synergy was assessed through MIC tests and time-kill studies, and binding affinities of nine β-lactams and BLIs to eight target receptors (L,D-transpeptidases [LDT] 1-5, D,D-carboxypeptidase, penicillin-binding protein [PBP] B, and PBP-lipo) were assessed using mass spectrometry and kinetic studies. Thermal stability and morphological changes were determined. Imipenem demonstrated high binding affinity to LDTs and PBPs, with extremely low inhibition constants (K_i,app; ≤0.002 mg/L for LDT1-2, ≤0.6 mg/L for PBPs), while cephalosporins, sulopenem, tebipenem, and amoxicillin exhibited moderate to low binding affinity. Durlobactam inactivated Bla_Mab and LDT/PBPs more potently than avibactam. The K_i,apps of durlobactam for PBP B, PBP-lipo, and LDT2 were below clinically achievable unbound concentrations, while avibactam's K_i,app for LDT/PBPs exceeded the clinical concentrations. Single β-lactam treatments resulted in minimal killing (~1 log₁₀ reduction). Although avibactam yielded no effect, combinations with avibactam showed a significant reduction (~4 log₁₀ CFU/mL). Durlobactam alone showed ~2 log₁₀ reduction, and when combined with imipenem or two β-lactams, durlobactam achieved near-eradication of Mab, surpassing the current therapy (amikacin + clarithromycin + imipenem/cefoxitin). Inactivation of PBP-lipo by sulopenem, imipenem, durlobactam, and amoxicillin (with avibactam) led to morphological changes, showing filaments. This study demonstrates the mechanistic basis of combinations therapy, particularly imipenem + durlobactam, in overcoming β-lactam resistance in Mab.

PMID:39714147 | PMC:PMC11823594 | DOI:10.1128/aac.01174-24

Anaerobe. 2025 Feb;91:102939. doi: 10.1016/j.anaerobe.2025.102939. Epub 2025 Jan 13.

ABSTRACT

The probing of live bacteria via the incorporation of fluorescent D-amino acids (FDAAs) during peptidoglycan synthesis has been shown to be practical for visualizing both gram-positive and gram-negative bacterial species. This study demonstrates the reliability and applications of FDAA labelling for the fluorescent imaging of an obligate anaerobe.

PMID:39814196 | DOI:10.1016/j.anaerobe.2025.102939

NPJ Vaccines. 2025 Jan 15;10(1):9. doi: 10.1038/s41541-024-01050-4.

ABSTRACT

Cyclic peptides are often used as scaffolds for the multivalent presentation of drug molecules due to their structural stability and constrained conformation. We identified a cyclic deca-peptide incorporating lipoamino acids for delivering T helper and B cell epitopes against group A Streptococcus (GAS), eliciting robust humoral immune responses. In this study, we assessed the function-immunogenicity relationship of the multi-component vaccine candidate (referred to as VC-13) to elucidate a mechanism of action. We identified a potential universal delivery platform, not only capable of adjuvanting different peptide epitopes (e.g., NS1 and 88/30 from group A Streptococcus, gonadotropin hormone releasing hormone [GnRH]), but also protein antigens (e.g., bovine serum albumin [BSA], receptor binding domain (RBD) of the SARS-CoV-2 protein responsible for COVID-19 infection [SARS-CoV-2 RBD]) and small molecular haptens (e.g., cocaine). All vaccine candidates self-assembled into sub-500 nm nanoparticles and induced high antigen-specific systemic IgG titers and opsonic potential compared to the antigen co-administered with a commercial adjuvant, complete Freund's adjuvant. Notably, presence of the cyclic decapeptide in this vaccine increased accumulation in the draining inguinal lymph nodes, facilitating cellular uptake of peptide antigens. Furthermore, the lipoamino acid promoted dendritic cell activation, acting as both toll-like receptors 2 and 4 -targeting moiety. Our study revealed the importance of the cyclic decapeptide and lipoamino acid presence in antigen presentation and immune response activation, leading onto the development of a fully synthetic, self-assembled, and promising platform for the delivery of subunit vaccines and anti-drug vaccines.

PMID:39809901 | PMC:PMC11733015 | DOI:10.1038/s41541-024-01050-4

Chemistry. 2025 Jan 13:e202500064. doi: 10.1002/chem.202500064. Online ahead of print.

ABSTRACT

Constrained peptides possess excellent properties for identifying lead compounds in drug discovery. While it has become increasingly straightforward to discover selective high-affinity peptide ligands, especially through genetically encoded libraries, their stability and bioavailability remain significant challenges. By integrating macrocyclization chemistry with bismuth binding, we generated series of linear, cyclic, bicyclic, and tricyclic peptides with identical sequences. Utilizing bismuth to rigidify the peptide structure allows for a better comparison of different constraint levels, reducing confounding effects of interactions often seen with hydrophobic stapling reagents. Our study facilitated the identification of a peptide-bismuth tricycle that fully withstands cellular levels of glutathione, acts as a nanomolar protease inhibitor without being proteolytically digested by its target, and is fully stable in human plasma. Importantly, this multicyclic peptide does not possess any non-canonical amino acid modifications. Using oxime ligation, we conjugated an analogue of this tricycle to the N-terminus of two nanobodies to demonstrate potential applications in targeted therapy.

PMID:39803821 | DOI:10.1002/chem.202500064

ACS Chem Biol. 2025 Jan 17;20(1):62-68. doi: 10.1021/acschembio.4c00629. Epub 2025 Jan 2.

ABSTRACT

As an important receptor in a host's immune and metabolic systems, NOD1 is usually activated by Gram-negative bacteria having meso-diaminopimelic acid (m-DAP) in their peptidoglycan (PGN). But some atypical Gram-positive bacteria also contain m-DAP in their PGN, giving them the potential to activate NOD1. The prevalence of m-DAP-type Gram-positive bacteria in the gut, however, remains largely unknown. Here, we report a stem-peptide-based m-DAP-containing tetrapeptide probe for labeling and identifying m-DAP-type Gram-positive microbiota. The probe was synthesized via a five-step convergent approach and demonstrated moderate selectivity toward m-DAP-type bacteria in vitro. In vivo labeling revealed that ∼13.7% of the mouse gut microbiota (mostly Gram-positive) was selectively labeled. We then identified Oscillibacter and several other Gram-positive genera in this population, most of which were previously unknown m-DAP-type bacteria. The following functional assay showed that Oscillibacter's PGN could indeed activate NOD1, suggesting an overlooked NOD1-activating role for these Gram-positive bacteria. These findings deepen our understanding of the structural diversity of gut microbes and their interactions with the host's immune system.

PMID:39745661 | DOI:10.1021/acschembio.4c00629