Marcos Pires

Nature Microbiology, Published online: 03 January 2025; doi:10.1038/s41564-024-01886-5

Peptidoglycan released by neighbouring kin or non-kin cell lysis induces physiological changes that protect from a range of stresses, including phage predation.

Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages ...

Nature Chemistry, Published online: 13 September 2024; doi:10.1038/s41557-024-01630-w

Biomolecular condensates compartmentalize molecules without membranes. Understanding condensate composition is important given that their function relies on the selective exclusion or enrichment of molecules. Now, investigating small-molecule partitioning reveals variations across compounds, yet correlations indicate physical similarities between disparate condensates. Machine learning accurately predicts partitioning on the basis of physicochemical features, demonstrating the role of a hydrophobic environment in driving enrichment and exclusion.

Optical imaging plays a central role in biology and medicine but is hindered by light scattering in live tissue. We report the counterintuitive observation that strongly absorbing molecules can achieve optical transparency in live animals. We explored ...

Nature Chemical Biology, Published online: 30 August 2024; doi:10.1038/s41589-024-01721-2

Pan et al. establish a general photoproximity labeling approach in living cells, applying microenvironment mapping with a HaloTag-based platform (HaloMap) to profile the stress granule proteome and identify ubiquitin-related modulators as key mediators of granule disassembly.

Nature Chemistry, Published online: 30 July 2024; doi:10.1038/s41557-024-01577-y

Tryptophan plays important biological roles in aromatic cages, such as methyllysine recognition, but the development of site-selective crosslinking to tryptophan is challenging. Now sulfonium can be used as a methyllysine mimic that binds to reader proteins and crosslinks tryptophan inside a pocket through single-electron transfer. This strategy enables the identification of methyllysine readers from the proteome.

Nature, Published online: 24 July 2024; doi:10.1038/s41586-024-07725-1

An ultra-rapid antimicrobial susceptibility testing method is introduced that bypasses the need for traditional blood culture, demonstrating the potential to significantly reduce the turnaround time of reporting drug susceptibility profiles.

Nature, Published online: 10 July 2024; doi:10.1038/s41586-024-07681-w

Edited bacteria were stably maintained in mouse gut for at least 42 days following the delivery of a base editor using an engineered phage-derived particle to modify Escherichia coli colonizing the gut.

Nature, Published online: 03 July 2024; doi:10.1038/s41586-024-07589-5

Evidence of modulated metallic and superconducting states stemming from an incommensurate structural stripe motif is reported in the bulk van der Waals superlattice SrTa2S5.

Nature Chemical Biology, Published online: 28 June 2024; doi:10.1038/s41589-024-01651-z

Keratinicyclins are recently discovered glycopeptide antibiotics. Now, the mechanism of action of keratinicyclin B has been uncovered. Keratinicyclin B displays narrow-spectrum inhibitory activity against Clostridioides difficile by binding a species-specific wall teichoic acid, disrupting cell wall protein localization and peptidoglycan remodeling.

Bacteria can repurpose their own bacteriophage viruses (phage) to kill competing bacteria. Phage-derived elements are frequently strain specific in their killing activity, although there is limited evidence that this specificity drives bacterial ...

Proceedings of the National Academy of Sciences, Volume 121, Issue 24, June 2024.

Wang, Torres et al. describe a probe for the live cell monitoring of nutrient uptake by Inverse Electron-Demand Diels–Alder reaction. By dually quenching a CFSE-probe that becomes fluorogenic after treatment with cytosolic esterases, and fluorescent upon reaction with strained alkenes, they could monitor uptake of fatty acids, sugars, and amino acids in primary immune cells.

Abstract

Cells rely heavily on the uptake of exogenous nutrients for survival, growth, and differentiation. Yet quantifying the uptake of small molecule nutrients at the single cell level is difficult. Here we present a new approach to studying the nutrient uptake in live single cells using Inverse Electron-Demand Diels Alder (IEDDA) chemistry. We have modified carboxyfluorescein-diacetate-succinimidyl esters (CFSE)—a quenched fluorophore that can covalently react with proteins and is only turned on in the cytosol of a cell following esterase activity—with a tetrazine. This tetrazine serves as a second quencher for the pendant fluorophore. Upon reaction with nutrients modified with an electron-rich or strained dienophile in an IEDDA reaction, this quenching group is destroyed, thereby enabling the probe to fluoresce. This has allowed us to monitor the uptake of a variety of dienophile-containing nutrients in live primary immune cell populations using flow cytometry and live-cell microscopy.

Proceedings of the National Academy of Sciences, Volume 121, Issue 19, May 2024.

Macrocycles are promising for drug development due to their good binding properties and the potential to cross membranes. A synthetic strategy and chemical building blocks are developed to produce and screen thousands of small, structurally highly diverse peptidic macrocycles. HTS identifies potent thrombin inhibitors with good membrane permeability. The strategy may be broadly applied in the development of membrane permeable therapeutics.

Abstract

Macrocycles offer an attractive format for drug development due to their good binding properties and potential to cross cell membranes. To efficiently identify macrocyclic ligands for new targets, methods for the synthesis and screening of large combinatorial libraries of small cyclic peptides were developed, many of them using thiol groups for efficient peptide macrocyclization. However, a weakness of these libraries is that invariant thiol-containing building blocks such as cysteine are used, resulting in a region that does not contribute to library diversity but increases molecule size. Herein, we synthesized a series of structurally diverse thiol-containing elements and used them for the combinatorial synthesis of a 2,688-member library of small, structurally diverse peptidic macrocycles with unprecedented skeletal complexity. We then used this library to discover potent thrombin and plasma kallikrein inhibitors, some also demonstrating favorable membrane permeability. X-ray structure analysis of macrocycle-target complexes showed that the size and shape of the newly developed thiol elements are key for binding. The strategy and library format presented in this work significantly enhance structural diversity by allowing combinatorial modifications to a previously invariant region of peptide macrocycles, which may be broadly applied in the development of membrane permeable therapeutics.

by Nisha Mahey, Rushikesh Tambat, Ritu Kalia, Rajnita Ingavale, Akriti Kodesia, Nishtha Chandal, Srajan Kapoor, Dipesh Kumar Verma, Krishan Gopal Thakur, Sanjay Jachak, Hemraj Nandanwar

Efflux pumps of the resistance-nodulation-cell division (RND) superfamily, particularly the AcrAB-TolC, and MexAB-OprM, besides mediating intrinsic and acquired resistance, also intervene in bacterial pathogenicity. Inhibitors of such pumps could restore the activities of antibiotics and curb bacterial virulence. Here, we identify pyrrole-based compounds that boost antibiotic activity in Escherichia coli and Pseudomonas aeruginosa by inhibiting their archetype RND transporters. Molecular docking and biophysical studies revealed that the EPIs bind to AcrB. The identified efflux pump inhibitors (EPIs) inhibit the efflux of fluorescent probes, attenuate persister formation, extend post-antibiotic effect, and diminish resistant mutant development. The bacterial membranes remained intact upon exposure to the EPIs. EPIs also possess an anti-pathogenic potential and attenuate P. aeruginosa virulence in vivo. The intracellular invasion of E. coli and P. aeruginosa inside the macrophages was hampered upon treatment with the lead EPI. The excellent efficacy of the EPI-antibiotic combination was evidenced in animal lung infection and sepsis protection models. These findings indicate that EPIs discovered herein with negligible toxicity are potential antibiotic adjuvants to address life-threatening Gram-negative bacterial infections.