Ribosome-targeting antibiotics and mechanisms of bacterial resistance

Polycarboxybetaine in advanced drug delivery systems: From structure-function relationship to therapeutic applications

Zwitterionic polycarboxybetaines (PCBs), combining quaternary ammonium cations and carboxylate anions in their repeating units, have emerged as promising materials for drug delivery applications. Their exceptional hydration, biocompatibility, and antifouling properties make them attractive alternatives to polyethylene glycol (PEG), particularly given growing concerns about immunogenicity of PEG. PCBs can be functionalized through various methods, including modification of side-chain moieties, adjustment of spacer length between charged groups, and incorporation of responsive elements. When applied to delivery drug, PCBs have been successfully developed into multiple formats including micelles, hydrogels, liposomes, and nanoparticles. Notably, in protein drug delivery, PCBs demonstrate significant advantages such as enhancing protein stability, extending circulation time, improving penetration through biological barriers, and reducing immunogenicity. Despite these promising features, several challenges remain, including complex synthesis requirements, limited mechanical properties, and pending FDA approval as pharmaceutical excipients. This review provides a comprehensive analysis of PCBs from the structure-function relationship, synthesis methods, and applications in drug delivery systems, while examining current limitations and future prospects.

Novel antibiotic discovery and the antibiotic resistome

INTRODUCTION

The success of antibiotics in the therapy of infectious diseases is overshadowed by almost inevitable emergence and dissemination of resistances toward these agents, which results in higher morbidity and mortality rates and increased costs. New strategies are now needed to both limit the risk of resistance and to discover new drugs that are efficacious.

AREAS COVERED

This review investigates the resistance problems through evolutionary lenses to better understand and potentially design improved therapeutics for infectious diseases. Furthermore, it gives an overview of the evolutionary history of antibiotic resistance genes and antibiotic biosynthesis genes/clusters, the structures of natural resistomes, and the regulatory roles of antibiotics. The author utilized ScienceDirect, PubMed, Web of Science and Google Scholar using the article's keywords and their combinations to retrieve the most relevant and up-to-date information.

EXPERT OPINION

Antibiotics and their corresponding resistances are ancient phenomena with their evolutionary timescales measured over a vast amount of time. Humans have also benefitted from access to, and the use of, a diverse range of antibiotics for many years also but have disrupted the balance by producing and using enormous amounts of antibiotics that have not existed before in natural ecosystems. This selective pressure has resulted in a tremendous expansion of resistomes. Future antibiotic discovery and development may need to pivot from exploiting extant antibiotic scaffolds and bacterial targets to reduce the risk of the rapid emergence of resistance from existing resistomes.

Molecular insights into de novo small-molecule recognition by an intron RNA structure

Despite the promise of vastly expanding the druggable genome, rational design of RNA-targeting ligands remains challenging as it requires the rapid identification of hits and visualization of the resulting cocomplexes for guiding optimization. Here, we leveraged high-throughput screening, medicinal chemistry, and structural biology to identify a de novo splicing inhibitor against a large and highly folded fungal group I intron. High-resolution cryoEM structures of the intron in different liganded states not only reveal molecular interactions that rationalize experimental structure-activity relationship but also shed light on a unique strategy whereby RNA-associated metal ions and RNA conformation exhibit exceptional plasticity in response to small-molecule binding. This study reveals general principles that govern RNA-ligand recognition, the interplay between chemical bonding specificity, and dynamic responses within an RNA target.

Biodegradation of ciprofloxacin by a manganese-oxidizing fungus Cladosporium sp. XM01: Performance and transcriptome analysis

Biogenic manganese (Mn) oxidation presents a promising approach for ciprofloxacin (CIP) removal from wastewater, yet the interaction between Mn bio-oxidation and CIP degradation remains unclear. The Mn-oxidizing fungus Cladosporium sp. XM01 was selected as a model strain in this study, to explore the impacts of CIP on microbial growth, function and biotransformation. Results showed that CIP exhibited a promotive effect on the growth and Mn(II) oxidation capacity of XM01. After 192 h of cultivation, 39.80 %-69.19 % of CIP was removed by XM01 in the absence of Mn(II), while over 84 % was removed with 300 μM Mn(II), demonstrating both direct and Mn(II)-enhanced indirect degradation of CIP. Transcriptomic analysis revealed that the upregulation of ribosome, peroxisome, and tyrosine metabolism pathways enhanced XM01's adaptation to CIP and supported microbial growth. Cytochrome P450 (CYP450) enzymes were implicated as key mediators in CIP degradation. Additionally, in the presence of Mn(II), the further upregulation of transmembrane transporters, NAD(P)H dehydrogenase, and CYP450 indicated that Mn bio-oxidation enhanced XM01's adaptation and response to CIP, thereby accelerating its degradation. Proposed CIP degradation pathways include piperazine epoxidation, decarboxylation, and hydroxylation. This study advances the understanding of fungal Mn oxidation in antibiotic removal, emphasizing its potential in wastewater treatment.

A critical view of antimicrobial peptides: exploring their potential and the barriers to realization

The global rise of multidrug-resistant infections highlights the urgent need for innovative therapeutic strategies beyond traditional antibiotics. Antimicrobial peptides (AMPs), naturally occurring in all forms of life and synthetically producible, have garnered significant attention for their broad-spectrum antimicrobial properties and diverse mechanisms of action, including membrane disruption, immune modulation, and biofilm formation inhibition and disruption. Despite great potential, the clinical deployment of AMPs faces significant challenges, including cytotoxicity, low chemical stability, high production costs, and stringent regulatory demands. Innovative strategies, such as AMP-antibiotic conjugation, offer potential solutions to some of these challenges by enhancing efficacy, reducing toxicity, and broadening antimicrobial activity. This review critically evaluates the promise and limitations of AMPs as therapeutic antibacterial agents. We also explore the potential of AMP-antibiotic conjugates, highlighting their potential synergistic effects and the obstacles to their clinical application. Antimicrobial self-assembling peptides are also discussed, with their ability to form nanostructures that may disrupt biofilms and inhibit bacterial communication, representing a promising but complex avenue. A critical evaluation of these emerging strategies, grounded in their practical applicability and translational challenges, is essential to drive meaningful progress in combating antimicrobial resistance.

Ligand-binding pockets in RNA and where to find them

RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules-via well-defined ligand-binding pockets-to modulate the regulatory repertoire of an RNA. The broad potential to modulate biological function intentionally via RNA-ligand interactions remains unrealized, however, due to challenges in identifying compact RNA motifs with the ability to bind ligands with good physicochemical properties (often termed drug-like). Here, we devise fpocketR, a computational strategy that accurately detects pockets capable of binding drug-like ligands in RNA structures. Remarkably few, roughly 50, of such pockets have ever been visualized. We experimentally confirmed the ligandability of novel pockets detected with fpocketR using a fragment-based approach introduced here, Frag-MaP, that detects ligand-binding sites in cells. Analysis of pockets detected by fpocketR and validated by Frag-MaP reveals dozens of sites able to bind drug-like ligands, supports a model for RNA secondary structural motifs able to bind quality ligands, and creates a broad framework for understanding the RNA ligand-ome.

Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis

The antibiotic resistance protein FusB rescues protein synthesis from inhibition by fusidic acid (FA), which locks elongation factor G (EF-G) to the ribosome after GTP hydrolysis. Here, we present time-resolved single-particle cryo-EM structures explaining the mechanism of FusB-mediated rescue. FusB binds to the FA-trapped EF-G on the ribosome, causing large-scale conformational changes of EF-G that break interactions with the ribosome, tRNA, and mRNA. This leads to dissociation of EF-G from the ribosome, followed by FA release. We also observe two independent binding sites of FusB on the classical-state ribosome, overlapping with the binding site of EF-G to each of the ribosomal subunits, yet not inhibiting tRNA delivery. The affinity of FusB to the ribosome and the concentration of FusB in S. aureus during FusB-mediated resistance support that direct binding of FusB to ribosomes could occur in the cell. Our results reveal an intricate resistance mechanism involving specific interactions of FusB with both EF-G and the ribosome, and a non-canonical release pathway of EF-G.

Streptomycin targets tumor-initiating cells by disrupting oxidative phosphorylation

Tumor initiating cells (TICs) are the roots of current shortcomings in advanced and metastatic cancer treatment. Endowed with self-renewal and multi-lineage differentiation capacity, TICs can disseminate and seed metastasis in distant organ. Our work identified streptomycin (SM), a potent bactericidal antibiotic, as a molecule capable of specifically targeting non-adherent TIC from colon and breast cancer cell lines. SM induces iron-dependent, reactive oxygen species (ROS)-mediated cell death, which is mechanistically distinct from RSL3-induced ferroptosis. SM-induced cell death is associated with profound alterations in mitochondrial morphology. This effect results from COX1 inhibition, which disrupts the regulation of the cytochrome c oxidase complex and triggers mitochondrial ROS production. SM's aldehyde group is essential, as its reduction into dihydrostreptomycin (DSM) abolishes its activity. These findings reveal a mechanism of action for streptomycin, shedding light on TIC metabolism and resistance, with potential implications for advanced cancer treatment.

Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics

Proteoforms are distinct molecular forms of proteins that act as building blocks of organisms, with post-translational modifications (PTMs) being one of the key changes that generate these variations. Mass spectrometry (MS)-based top-down proteomics (TDP) is the leading technology for proteoform identification due to its preservation of intact proteoforms for analysis, making it well-suited for comprehensive PTM characterization. A crucial step in TDP is searching MS data against a database of candidate proteoforms. To extend the reach of TDP to organisms with limited PTM annotations, we developed Proteoform-predictor, an open-source tool that integrates homology-based PTM site prediction into proteoform database creation. The new tool creates databases of proteoform candidates after registration of homologous sequences, transferring PTM sites from well-characterized species to those with less comprehensive proteomic data. Our tool features a user-friendly interface and intuitive workflow, making it accessible to a wide range of researchers. We demonstrate that Proteoform-predictor expands proteoform databases with tens of thousands of proteoforms for three bacterial strains by comparing them to the reference proteome of Escherichia coli (E. coli) K12. Subsequent TDP analysis for Serratia marcescens (S. marcescens) and Salmonella typhimurium (S. typhimurium) demonstrated significant improvement in protein and proteoform identification, even for proteins with variant sequences. As TDP technology advances, Proteoform-predictor will become an important tool for expanding the applicability of proteoform identification and PTM biology to more diverse species across the phylogenetic tree of life.

Macrolide resistance in Mycobacterium abscessus: current insights and future perspectives

Mycobacterium abscessus (MAB) is a rapidly growing, non-tuberculous mycobacterium that has emerged as a significant pathogen in both pulmonary and extrapulmonary infections. It is rising in prevalence, especially among individuals with underlying lung conditions such as cystic fibrosis and chronic obstructive pulmonary disease, highlighting its growing clinical importance. The treatment of MAB infections is notoriously challenging due to intrinsic resistance to many antibiotics and low cure rates, typically <50%. Macrolides are a cornerstone in the treatment of MAB infections because regimens that include effective macrolide therapy are associated with higher cure rates. However, MAB possesses intrinsic and acquired drug resistance mechanisms against macrolides, complicating drug susceptibility testing and selection of highly effective treatment regimens. This review aims to provide a summary of the current understanding of macrolide resistance mechanisms in MAB. We explored the epidemiology of resistance in different countries and the molecular mechanisms involved. We have highlighted the variability in sensitivity of existing markers to predict phenotypic macrolide drug resistance across different countries, suggesting the involvement of unknown resistance mechanisms. By synthesizing current knowledge and identifying gaps in the literature, this review seeks to inform clinical practice and guide future research efforts in the fight against MAB drug resistance.

Light-driven self-sterilizing cotton fabric and drug delivery: improvement of the antimicrobial activity of 4-sulfo-1,8-naphthalimide via its dendrimer and metallic dendrimer formation

The search for new bioactive substances with microbiological activity is dictated by the increasing resistance of the drugs used in clinical practice against various pathogenic microorganisms. In this respect, particular attention is paid to the modified dendrimers with biologically active substances and their metal complexes. This work describes synthesizing and characterizing a new copper complex of first-generation polypropylene imine (PPI) dendrimer, modified with 4-sulfo-1,8-naphthalimide. The new metallodendrimer [Cu2(E)(NO3)4] has been characterized by IR and electron paramagnetic resonance (EPR) spectroscopy. Two copper ions were found to form a complex with the dendrimer ligand. Cotton fabrics were treated with the dendrimer ligand (E), its monomer structural analog (M), and metallodendrimer. The microbiological activity of the three compounds and the treated cotton fabrics with them has been tested in the dark and after light irradiation against bacterial strains: Gram-positive B. cereus and Gram-negative P. aeruginosa. The results showed that the metallodendrimer was slightly more effective than the dendrimer ligand E and monomer M, and their activity was enhanced after light irradiation. The increase in antimicrobial activity after light irradiation was due to the generation of highly reactive singlet oxygen, which damages bacteria's cell membrane, leading to their inactivation. The similar activity against both types of bacteria indicates that all three compounds can be classified as broad-spectrum antimicrobial agents. The virucidal effects of the studied compounds were also tested against human adenovirus type 5 (HAdV5) and human respiratory syncytial virus (HRSV-S2) after 30 min/60 min. The newly synthesized compounds showed no activity against HAdV-5, but the activity against HSV-2 viruses increases with the prolongation of their interaction.

Altering translation allows E. coli to overcome G-quadruplex stabilizers

G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses reveal decreased protein and transcript levels, respectively, for ribosome assembly factors and proteins associated with translation in the presence of G4 stabilizer. Our results support a model in which reducing the rate of translation by altering translation initiation, translation elongation, or ribosome assembly can compensate for G4-related stress in E. coli.

Unraveling tetracycline and its degradation product: Induction mechanisms of antibiotic resistance in Escherichia coli

In aquatic environments, antibiotics degrade into byproducts, potentially enhancing bacterial resistance. However, the specific mechanisms by which these byproducts induce bacterial resistance remain elusive. This study conducted experimental evolution experiments to explore how E. coli adapts to tetracycline (TC) and its primary degradation products-anhydrotetracycline (ATC), epitetracycline (ETC), and 4-epianhydrotetracycline (EATC)-through evolution experiments. Prolonged exposure to TC and its byproducts significantly increased frequency of resistant mutants in E. coli ATCC25922, with a maximum 106-fold increase. Resistant mutants exhibited markedly elevated minimum inhibitory concentrations (MICs) for TC, ampicillin (AMP), and ciprofloxacin (CIP), indicating multidrug resistance. Transcriptomic analysis showed that the antibiotic resistance phenotype could be related to enhanced target protection, metabolic adaptations, and reduced membrane permeability. The induction pathways between TC and its byproducts were distinct. Specifically, TC20d (where TC20d represents the mutants collected after 20 days of continuous exposure to TC) was associated with more alterations in ribosome-associated genes, which was correlated with an enhanced defensive response as shown by the data. Moreover, variations in energy metabolism gene expression suggest a robust metabolic defense in ATC20d and ETC20d. When TC and its byproducts-ATC, ETC, and EATC-act together, they induce antibiotic resistant mutants at rates of 29.8 %, 18.9 %, 18.3 %, and 31.9 %, respectively. This study provides a descriptive overview of the possible adaptive mechanisms and pathways that may be involved in antibiotic resistance due to environmental exposure.

Ligand-binding pockets in RNA, and where to find them

RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules - via well-defined ligand binding pockets - to modulate the regulatory repertoire of an RNA. The broad potential to modulate biological function intentionally via RNA-ligand interactions remains unrealized, however, due to challenges in identifying compact RNA motifs with the ability to bind ligands with good physicochemical properties (often termed drug-like). Here, we devise fpocketR, a computational strategy that accurately detects pockets capable of binding drug-like ligands in RNA structures. Remarkably few, roughly 50, of such pockets have ever been visualized. We experimentally confirmed the ligandability of novel pockets detected with fpocketR using a fragment-based approach introduced here, Frag-MaP, that detects ligand-binding sites in cells. Analysis of pockets detected by fpocketR and validated by Frag-MaP reveals dozens of newly identified sites able to bind drug-like ligands, supports a model for RNA secondary structural motifs able to bind quality ligands, and creates a broad framework for understanding the RNA ligand-ome.

The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation

During bacterial translation initiation, the 30S ribosomal subunit, initiation factors, and initiator tRNA define the reading frame of the mRNA. This process is inhibited by kasugamycin, edeine and GE81112, however, their mechanisms of action have not been fully elucidated. Here we present cryo-electron microscopy structures of 30S initiation intermediate complexes formed in the presence of kasugamycin, edeine and GE81112 at resolutions of 2.0-2.9 Å. The structures reveal that all three antibiotics bind within the E-site of the 30S and preclude 30S initiation complex formation. While kasugamycin and edeine affect early steps of 30S pre-initiation complex formation, GE81112 stalls pre-initiation complex formation at a further step by allowing start codon recognition, but impeding IF3 departure. Collectively, our work highlights how chemically distinct compounds binding at a conserved site on the 30S can interfere with translation initiation in a unique manner.

Microneedle technology for enhanced topical treatment of skin infections

Skin infections caused by microbes such as bacteria, fungi, and viruses often lead to aberrant skin functions and appearance, eventually evolving into a significant risk to human health. Among different drug administration paradigms for skin infections, microneedles (MNs) have demonstrated superiority mainly because of their merits in enhancing drug delivery efficiency and reducing microbial resistance. Also, integrating biosensing functionality to MNs offers point-of-care wearable medical devices for analyzing specific pathogens, disease status, and drug pharmacokinetics, thus providing personalized therapy for skin infections. Herein, we do a timely update on the development of MN technology in skin infection management, with a special focus on how to devise MNs for personalized antimicrobial therapy. Notably, the advantages of state-of-the-art MNs for treating skin infections are pointed out, which include hijacking sequential drug transport barriers to enhance drug delivery efficiency and delivering various therapeutics (e.g., antibiotics, antimicrobial peptides, photosensitizers, metals, sonosensitizers, nanoenzyme, living bacteria, poly ionic liquid, and nanomoter). In addition, the nanoenzyme-based multimodal antimicrobial therapy is highlighted in addressing intractable infectious wounds. Furthermore, the MN-based biosensors used to identify pathogen types, track disease status, and quantify antibiotic concentrations are summarized. The limitations of antimicrobial MNs toward clinical translation are offered regarding large-scale production, quality control, and policy guidance. Finally, the future development of biosensing MNs with easy-to-use and intelligent properties and MN-based wearable drug delivery for home-based therapy are prospected. We hope this review will provide valuable guidance for future development in MN-mediated topical treatment of skin infections.

Phosphate Limitation Enhances Heterologous Enzyme Production in Bacillus subtilis: Mechanistic Insights and Universal Applicability

Bacillus subtilis is one of the commonly used hosts for heterologous enzyme expression, depending on media rich in carbon, nitrogen, and phosphate sources for optimal growth and enzyme production. Interestingly, our investigation of maltotetraose-forming amylase, a key enzyme for efficient maltotetraose synthesis, revealed that phosphate limitation significantly enhances the growth rate and production of heterologous enzymes in recombinant B. subtilis. Under phosphate-limited conditions in a 15 L fermenter, the enzyme activity reached 679.15 U/mL, an improvement of 101% over the initial levels and a 12 h reduction in fermentation time. Transcriptomic analysis indicated that phosphate limitation promotes sustained enzyme production by upregulating protein synthesis and quality control pathways while optimizing energy utilization. This strategy was validated across various enzyme systems, highlighting its general applicability for enhancing heterologous protein expressions. These findings provide valuable insights for the industrial production of maltotetraose-forming amylase and other high-value enzymes, supporting the advancement of microbial fermentation technology.

Development of a novel chimeric lysin to combine parental phage lysin and cefquinome for preventing sow endometritis after artificial insemination

Sow endometritis is usually caused by multiple species of pathogenic bacteria. Numerous isolates from endometritis patients have developed antimicrobial resistance. Thus, novel antibacterial agents and strategies to combat endometritis are needed. A total of 526 bacteria, including Staphylococcus spp. (26.3%), Streptococcus spp. (12.3%), E. coli (28.9%), Enterococcus spp. (20.1%), Proteus spp. (9.5%), and Corynebacterium spp. (2.8%), were isolated from sows with endometritis. We constructed a novel chimeric lysin, ClyL, which is composed of a cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP) catalytic domain from the phage lysin LysGH15 and a cell wall-binding domain (CBD) from the prophage lysin Lys0859. The activities of ClyL and Lys0859 were most pronounced for the Staphylococcus and Streptococcus strains isolated from sow endometritis and bovine mastitis, respectively. ClyL and Lys0859 were combined to create a phage lysin cocktail, which demonstrated a synergistic effect against the coinfection of Staphylococcus and Streptococcus in vitro and in vivo. Furthermore, the combination of phage lysin cocktail and cefquinome had a synergistic bactericidal effect on boar semen that did not influence the activity of sperm. Remarkably, the incidence rate of sow endometritis was 0% (0/7) when the combination of phage lysin cocktail and cefquinome was used in semen via artificial insemination compared with 50% (3/6) when PBS was administered. Overall, the administration of a phage lysin cocktail and cefquinome in semen via artificial insemination is a promising novel strategy to prevent sow endometritis after artificial insemination.

NIR-Activated Hydrogel with Dual-Enhanced Antibiotic Effectiveness for Thorough Elimination of Antibiotic-Resistant Bacteria

Antibiotic resistance has become a critical health crisis globally. Traditional strategies using antibiotics can lead to drug-resistance, while inorganic antimicrobial agents can cause severe systemic toxicity. Here, we have developed a dual-antibiotic hydrogel delivery system (PDA-Ag@Levo/CMCS), which can achieve controlled release of clinical antibiotics levofloxacin (Levo) and classic nanoscale antibiotic silver nanoparticles (AgNPs), effectively eliminating drug-resistant P. aeruginosa. Benefiting from the photothermal (PTT) effect of polydopamine (PDA), the local high temperature generated by PDA-Ag@Levo/CMCS can quickly kill bacteria through continuous and responsive release of dual-antibiotics to restore sensitivity to ineffective antibiotics. Moreover, AgNPs could significantly improve the efficiency of traditional antibiotics by disrupting bacterial membranes and reducing their toxicity to healthy tissues. A clever combination of PTT and drug-combination therapy can effectively eliminate biofilms and drug-resistant bacteria. Mechanism studies have shown that PDA-Ag@Levo might eliminate drug-resistant P. aeruginosa by disrupting biofilm formation and protein synthesis, and inhibit the resistance mutation of P. aeruginosa by promoting the expression of related genes, such as rpoS, dinB, and mutS. Collectively, the synergistic effect of this dual-antibiotic hydrogel combined with PTT provides a creative strategy for eliminating drug-resistant bacteria in chronic infection wounds.

Metabolic analysis of the mode of action and mode of resistance of fusidic acid against Staphylococcus aureus

Understanding bacterial responses to antibiotics is essential for identifying resistance mechanisms and developing novel therapies. This study evaluated the resistance of Staphylococcus aureus (S. aureus) to fusidic acid (FD) in 100 patients with skin and soft tissue infections (SSTIs), revealing susceptibility to FD despite resistance to other antibiotics. Through adaptive laboratory evolution, we developed a highly FD-resistant strain, E10, and identified three gene mutations (fusA, BPENGOFF-00211, and rplF) using whole-genome sequencing. The fusA mutation was the primary contributor to resistance. Furthermore, the evolved fusA mutant strain (H457Y) displayed impaired coagulation function and reduced growth rates. We also analyzed the metabolomic profiles of ancestral ATCC 25923 and evolved E10 strains, both treated and untreated with FD, revealing that the fusA gene can independently induce metabolic reprogramming. These changes primarily impacted pathways involved in central carbon metabolism, nucleotide metabolism, and amino acid synthesis. This study highlights the complexity of FD resistance in S. aureus and offers insights into the metabolic pathways associated with antibiotic resistance.

Improving Cellular Protein Content of Saccharomyces cerevisiae Based on Adaptive Evolution and Flow Cytometry-Aided High Throughput Screening

Enhancing the protein content and production efficiency of Saccharomyces cerevisiae is crucial as an alternative protein source. This study screened nongenetically modified yeast strains with high protein content for food ingredient production and explored the underlying mechanisms. Yeast protein levels were found to correlate with RNA, leading to a high-throughput screening method using RNA fluorescence and flow cytometry. Four mutant libraries (∼200,000 cells) were generated through adaptive laboratory evolution in protein synthesis inhibitors, resulting in the high protein mutant content B1, with a protein content of 65.8 g/100 g dry cell weight in shake flasks. In a 45 L bioreactor using fed-batch fermentation with ethanol below 1.5 g/L, B1's protein content increased to 70.3 g/100 g dry cell weight, an 18.5% rise. Mannan and β-glucan levels in the cell wall decreased by 21.7 and 30.5%, potentially enhancing protein extraction for food production. Transcriptome analysis revealed that increased protein content results from down-regulating the cell cycle and meiosis-related genes. Validation of differentially expressed genes demonstrated that up-regulating SUT1 and down-regulating CNM67 are key for enhancing protein synthesis and accumulation. This study proposes a nongenetic screening method for high protein content S. cerevisiae strains, achieving the highest reported protein content.

A Universal Support for the Solid-Phase Synthesis of Peptidyl-tRNA Mimics

Hydrolysis-resistant RNA-peptide conjugates that mimic peptidyl-tRNAs are often required for structural and functional studies of protein synthesis at the ribosome. These conjugates can be synthesized by solid-phase chemical synthesis, which allows maximum flexibility in both the peptide and RNA sequence. The commonly used strategy is based on (3'-N-aminoacyl)-3'-amino-3'-deoxyadenosine solid supports, which already contain the first C-terminal amino acid of the target peptidyl chain. This is a limitation in the sense that different individual supports must be synthesized for different C-terminal amino acids. In this study, we demonstrate a solution to this problem by introducing a novel universal support. The key is a free ribose 3'-NH2 group that can be coupled to any amino acid. This is made possible by a photocleavable ether moiety that links the ribose 2'-O to the support, thus avoiding the typical O-to-N migration that occurs when using 2'-O-acyl linked solid supports. Once assembled, the conjugate is readily cleaved by UV irradiation. The structural integrity of the obtained peptidyl-RNA conjugates was verified by mass spectrometry analysis. In conclusion, the new photocleavable solid support makes the synthesis of 3'-peptidyl tRNA mimics of different peptidyl chains significantly more efficient compared to the commonly used approaches.

Metabolic rearrangement enables adaptation of microbial growth rate to temperature shifts

Temperature is a key determinant of microbial behaviour and survival in the environment and within hosts. At intermediate temperatures, growth rate varies according to the Arrhenius law of thermodynamics, which describes the effect of temperature on the rate of a chemical reaction. However, the mechanistic basis for this behaviour remains unclear. Here we use single-cell microscopy to show that Escherichia coli exhibits a gradual response to temperature upshifts with a timescale of ~1.5 doublings at the higher temperature. The response was largely independent of initial or final temperature and nutrient source. Proteomic and genomic approaches demonstrated that adaptation to temperature is independent of transcriptional, translational or membrane fluidity changes. Instead, an autocatalytic enzyme network model incorporating temperature-sensitive Michaelis-Menten kinetics recapitulates all temperature-shift dynamics through metabolome rearrangement, resulting in a transient temperature memory. The model successfully predicts alterations in the temperature response across nutrient conditions, diverse E. coli strains from hosts with different body temperatures, soil-dwelling Bacillus subtilis and fission yeast. In sum, our model provides a mechanistic framework for Arrhenius-dependent growth.

Targeting noncoding RNAs to treat atherosclerosis

Noncoding RNAs (ncRNAs) are pivotal for various pathological processes, impacting disease progression. The potential for leveraging ncRNAs to prevent or treat atherosclerosis and associated cardiovascular diseases is of great significance, especially given the increasing prevalence of atherosclerosis in an ageing and sedentary population. Together, these diseases impose a substantial socio-economic burden, demanding innovative therapeutic solutions. This review explores the potential of ncRNAs in atherosclerosis treatment. We commence by examining approaches for identifying and characterizing atherosclerosis-associated ncRNAs. We then delve into the functional aspects of ncRNAs in atherosclerosis development and progression. Additionally, we review current RNA and RNA-targeting molecules in development or under approval for clinical use, offering insights into their pharmacological potential. The importance of improved ncRNA delivery strategies is highlighted. Finally, we suggest avenues for advanced research to accelerate the use of ncRNAs in treating atherosclerosis and mitigating its societal impact. LINKED ARTICLES: This article is part of a themed issue Non-coding RNA Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v182.2/issuetoc.

Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine

The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, leaving only three protein-coding genes and highly fragmented mitoribosomal rRNAs, raising challenging questions about mitoribosome composition, assembly and structure. Our study reveals how Toxoplasma gondii assembles over 40 mt-rRNA fragments using exclusively nuclear-encoded mitoribosomal proteins and three lineage-specific families of RNA-binding proteins. Among these are four proteins from the Apetala2/Ethylene Response Factor (AP2/ERF) family, originally known as transcription factors in plants and Apicomplexa, now repurposed as essential mitoribosome components. Cryo-EM analysis of the mitoribosome structure demonstrates how these AP2 proteins function as RNA binders to maintain mitoribosome integrity. The mitoribosome is also decorated with members of lineage-specific RNA-binding proteins belonging to RAP (RNA-binding domain abundant in Apicomplexa) proteins and HPR (heptatricopeptide repeat) families, highlighting the unique adaptations of these parasites. Solving the molecular puzzle of apicomplexan mitoribosome could inform the development of therapeutic strategies targeting organellar translation.

Geographic Distribution Pattern Determines Soil Microbial Community Assembly Process in Acanthopanax senticosus Rhizosphere Soil

The geographic distribution patterns of soil microbial communities associated with cultivated Acanthopanax senticosus plants in Northeast China were investigated. High-throughput sequencing revealed that the diversity and community assembly of bacterial and fungal communities in the inter-root soil varied significantly with geographic location. The study found that bacterial communities were predominantly assembled through stochastic processes at most sites, while fungal communities showed greater variation, with both stochastic and deterministic processes involved. The complexity of bacterial-fungal co-occurrence networks also varied with longitude and latitude, demonstrating both positive and negative interactions. PICRUSt 2.0 and FUNGuild were used to predict the potential functions of soil bacterial and fungal microbiota, respectively, during different land use patterns. The average taxonomic distinctness (AVD) index indicated varying degrees of community stability across sites. Key microbial taxa contributing to community variability were identified through Random Forest modeling, with Bacteriap25 and Sutterellaceae standing out among bacteria, and Archaeorhizomyces and Clavaria among fungi. Soil chemical properties, including pH, TN, TP, EC, and SOC, significantly correlated with microbial diversity, composition, and co-occurrence networks. Structural equation modeling revealed that geographic distribution patterns directly and indirectly influenced soil chemical properties and microbial communities. Overall, the study provides insights into the geographic distribution patterns of soil microbial communities associated with A. senticosus and highlights the need for further research into the underlying mechanisms shaping these patterns.

Ultrafast Evolution of Bacterial Antimicrobial Resistance by Picoliter-Scale Centrifugal Microfluidics

Experimental evolution is a powerful approach for scrutinizing and dissecting the development of antimicrobial resistance; nevertheless, it typically demands an extended duration to detect evolutionary changes. Here, a centrifugal microfluidics system is designed to accelerate the process. Through a simple step of on-chip centrifugation, a highly condensed bacterial matrix of ∼1012 cells/mL at the enrichment tip of the chip channel is derived, enabling bacteria encapsulated to survive in antimicrobial concentrations several times higher than the minimum inhibitory concentration (MIC) and rapidly develop resistance in the first 10 h. After 48 h of on-chip evolution, the E. coli strain demonstrated a 64 to 128-fold reduction in sensitivity to disinfectants (triclosan) as well as antibiotics (ciprofloxacin and amikacin), a rate substantially swifter compared to conventional continuous inoculation-based experimental evolution. The speed and simplicity of this microfluidic system suggest its broad application for uncovering resistance mechanisms and identifying targets of biocides and antibiotics.

Chemical strategies for antisense antibiotics

Antibacterial resistance is a severe threat to modern medicine and human health. To stay ahead of constantly-evolving bacteria we need to expand our arsenal of effective antibiotics. As such, antisense therapy is an attractive approach. The programmability allows to in principle target any RNA sequence within bacteria, enabling tremendous selectivity. In this Tutorial Review we provide guidelines for devising effective antibacterial antisense agents and offer a concise perspective for future research. We will review the chemical architectures of antibacterial antisense agents with a special focus on the delivery and target selection for successful antisense design. This Tutorial Review will strive to serve as an essential guide for antibacterial antisense technology development.

Small Molecule RNA Degraders

RNA is a central molecule in life, involved in a plethora of biological processes and playing a key role in many diseases. Targeting RNA emerges as a significant endeavor in drug discovery, diverging from conventional protein-centric approaches to tackle various pathologies. Whilst identifying small molecules that bind to specific RNA regions is the first step, the abundance of non-functional RNA segments renders many interactions biologically inert. Consequently, small molecule binding does not necessarily meet stringent criteria for clinical translation, calling for solutions to push the field forward. Converting RNA-binders into RNA-degraders presents a promising avenue to enhance RNA-targeting. This mini-review outlines strategies and exemplars wherein simple small molecule RNA binders are reprogrammed into active degraders through the linkage of functional groups. These approaches encompass mechanisms that induce degradation via endogenous enzymes, termed RIBOTACs, as well as those with functional moieties acting autonomously to degrade RNA. Through this exploration, we aim to offer insights into advancing RNA-targeted therapeutic strategies.

Novel pleuromutilin derivatives conjugated with phenyl-sulfide and boron-containing moieties as potent antibacterial agents against antibiotic-resistant bacteria

In response to the escalating threat of microbial resistance, a series of novel pleuromutilin derivatives, conjugated with phenyl-sulfide and boron-containing moieties, were designed and synthesized. Most derivatives, especially 14b and 16b, demonstrated significant efficacy against Gram-positive bacteria, including multidrug-resistant strains, as well as pleuromutilin-resistant strains. Compound 16b showed high stability in the liver microsomes of rats and humans, along with acceptable tolerance in vitro and in vivo. Additionally, compound 16b exhibited promising efficacy in MRSA-infected mouse models. Our data highlight the potential of conjugated pleuromutilin derivatives as valuable agents against drug-resistant bacteria.

Three Stages of Nascent Protein Translocation Through the Ribosome Exit Tunnel

All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and recycling. In fact, peptide bonds are formed only during the elongation phase, which comprises periodic association of transfer RNAs and multiple auxiliary proteins with the ribosome and the addition of an amino acid to the nascent polypeptide one at a time. The protein spends a considerable amount of time attached to the ribosome. Here, we conceptually divide this portion of the protein lifetime into three stages. We define each stage on the basis of the position of the N-terminus of the nascent polypeptide within the ribosome exit tunnel and the context of the catalytic center. We argue that nascent polypeptides experience a variety of forces that determine how they translocate through the tunnel and interact with the tunnel walls. We review current knowledge about nascent polypeptide translocation and identify several white spots in our understanding of the birth of proteins.

Mechanism of staphylococcal resistance to clinically relevant antibiotics

Staphylococcus aureus, a notorious pathogen with versatile virulence, poses a significant challenge to current antibiotic treatments due to its ability to develop resistance mechanisms against a variety of clinically relevant antibiotics. In this comprehensive review, we carefully dissect the resistance mechanisms employed by S. aureus against various antibiotics commonly used in clinical settings. The article navigates through intricate molecular pathways, elucidating the mechanisms by which S. aureus evades the therapeutic efficacy of antibiotics, such as β-lactams, vancomycin, daptomycin, linezolid, etc. Each antibiotic is scrutinised for its mechanism of action, impact on bacterial physiology, and the corresponding resistance strategies adopted by S. aureus. By synthesising the knowledge surrounding these resistance mechanisms, this review aims to serve as a comprehensive resource that provides a foundation for the development of innovative therapeutic strategies and alternative treatments for S. aureus infections. Understanding the evolving landscape of antibiotic resistance is imperative for devising effective countermeasures in the battle against this formidable pathogen.

Ribosomal A site binding pattern differs between Arm methyltransferases from clinical pathogens and a natural producer of aminoglycosides

The extensive use of aminoglycosides to treat bacterial infections has led to significant resistance, posing a global health threat. Recent clinical reports highlight high levels of aminoglycoside resistance due to Arm/Kam methyltransferases, which methylate specific nucleotides in 16S rRNA, preventing antibiotic binding to the ribosome. This study compared the ribosomal A site binding patterns of Arm methyltransferases from clinical pathogens (ArmA, RmtB, RmtC, and RmtD) with those of the Sgm methyltransferase from a natural aminoglycoside producer. We introduced single mutations near the G1405 nucleotide in helix 44 of 16S rRNA to assess their impact on the methylation ability of Arm methyltransferases in E. coli cells with homogeneous mutant ribosomes. We evaluated how these mutations affected bacterial viability in cells with mixed and homogeneous ribosome populations and determined the minimal inhibitory concentration of kanamycin to assess their impact on Arm enzyme activity. Notably, Sgm methyltransferase exhibited a distinct methylation pattern compared to Arm methyltransferases from clinical strains. Structural comparisons of Sgm, RmtB, and RmtC revealed different spatial orientations of key amino acids involved in ribosomal binding, highlighting evolutionary differences. This research enhances understanding of Arm methyltransferases and lays the groundwork for designing inhibitors to combat this potent form of antibiotic resistance.

Effects of bile acids on the growth, composition and metabolism of gut bacteria

Bile acids (BAs) exert a profound influence on the body's pathophysiology by intricately shaping the composition of gut bacteria. However, the complex interplay between BAs and gut microbiota has impeded a systematic exploration of their impact on intestinal bacteria. Initially, we investigated the effects of 21 BAs on the growth of 65 gut bacterial strains in vitro. Subsequently, we examined the impact of BAs on the overall composition of intestinal bacteria, both in vivo and in vitro. The results unveiled distinct effects of various BAs on different intestinal strains and their diverse impacts on the composition of gut bacteria. Mechanistically, the inhibition of intestinal strains by BAs occurs through the accumulation of these acids within the strains. The intracellular accumulation of deoxycholic acid (DCA) significantly influenced the growth of intestinal bacteria by impacting ribosome transcription and amino-acid metabolism. The metabolomic analysis underscores the pronounced impact of DCA on amino-acid profiles in both in vivo and in vitro settings. This study not only elucidates the effects of BAs on a diverse range of bacterial strains and their role in shaping the gut microbiota but also reveals underlying mechanisms essential for understanding and maintaining a healthy gut microbiota.

Unveiling mechanisms of antimicrobial peptide: Actions beyond the membranes disruption

Antimicrobial peptides (AMPs) are a critical component of the innate immune system, playing a key role in defending against a variety of pathogenic microorganisms. While many AMPs act primarily on the cell membrane of target pathogens, leading to lysis and subsequent cell death, less is known about their nonlytic membrane activity. This nonlytic activity allows AMPs to target and disrupt bacterial cells without causing lysis, leading to bacterial death through alternative mechanisms.Understanding these nonlytic properties of AMPs is crucial, as they present a promising alternative to traditional antibiotics, which can induce bacterial resistance and have adverse effects on human health and the environment. The mechanisms by which AMPs exhibit nonlytic membrane activity are still being explored. However, it is believed that AMPs penetrate the bacterial membrane and interact directly with internal cellular components such as DNA, RNA, and various enzymes essential for microbial survival and replication. This interaction disrupts metabolic homeostasis, ultimately resulting in bacterial death.The nonlytic activity of AMPs also results in minimal damage to host cells and tissues, making them attractive candidates for the development of new, more effective antibiotics. This review emphasizes the mechanisms by which AMPs nonlytically target cellular components, including DNA, proteins, RNA, and other biomolecules, and discusses their clinical significance. Understanding these mechanisms may pave the way for developing alternatives to conventional antibiotics, offering a solution to the growing issue of antibiotic resistance.

Microbial-derived peptides with anti-mycobacterial potential

Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis, has become the leading cause of death. The subsequent emergence of multidrug-resistant, extensively drug-resistant and totally drug-resistant strains, brings an urgent need to discover novel anti-TB drugs. Among them, microbial-derived anti-mycobacterial peptides, including ribosomally synthesized and post-translationally modified peptides (RiPPs) and multimodular nonribosomal peptides (NRPs), now arise as promising candidates for TB treatment. This review presents 96 natural RiPP and NRP families from bacteria and fungi that have broad spectrum in vitro activities against non-resistant and drug-resistant mycobacteria. In addition, intracellular targets of 22 molecules are the subject of much attention. Meanwhile, chemical features of 38 families could be modified in order to improve properties. In final, structure-activity relationships suggest that the modifications of various groups, especially the peptide side chains, the amino acid moieties, the cyclic peptide skeletons, various special groups, stereochemistry and entire peptide chain length are important for increasing the potency.

Design, synthesis and structure-activity relationships of novel non-ketolides: 9-Oxime clarithromycin featured with seven-to thirteen-atom-length diamine linkers at 3-OH

We report here on the structure-activity relationships of hybrids combining 3-descladinosyl clarithromycin with quinolones linked by extended diamine connectors. Several hybrids, exemplified by 23Bc, 23Be, 23Bf, 26Be, and 30Bc, not only restored potency against inducibly resistant pathogens but also exhibited significantly enhanced activities against constitutively resistant strains of Staphylococcus pneumoniae and Staphylococcus pyogenes, which express high-level resistance independent of clarithromycin or erythromycin induction. Additionally, the novel hybrids showed susceptibility against Gram-negative Haemophilus influenzae. Notably, hybrid 23Be demonstrated dual modes of action by inhibiting both protein synthesis and DNA replication in vitro and in vivo. Given these promising characteristics, 23Be emerges as a potential candidate for the treatment of community-acquired bacterial pneumonia.

Design and structure-activity relationships of ether-linked alkylides: Hybrids of 3-O-descladinosyl macrolides and quinolone motifs

Ketolides (3-keto) such as TE-802 and acylides (3-O-acyl) like TEA0929 are ineffective against constitutively resistant pathogens harboring erythromycin ribosomal methylation (erm) genes. Following our previous work on alkylides (3-O-alkyl), we explored the structure-activity relationships of hybrids combining (R/S) 3-descladinosyl erythromycin with 6/7-quinolone motifs, featuring extended ether-linked spacers, with a focus on their efficacy against pathogens bearing constitutive erm gene resistance. Optimized compounds 17a and 31f not only reinstated efficacy against inducibly resistant pathogens but also demonstrated significantly augmented activities against constitutively resistant strains of Streptococcus pneumoniae and Streptococcus pyogenes, which are typically refractory to existing C-3 modified macrolides. Notably, hybrid 31f (coded ZN-51) represented a pioneering class of agents distinguished by its dual modes of action, with ribosomes as the primary target and topoisomerases as the secondary target. As a novel chemotype of macrolide-quinolone hybrids, alkylide 31f is a valuable addition to our armamentarium against macrolide-resistant bacteria.

Ellagic acid-modified gold nanoparticles to combat multi-drug resistant bacterial infections in vitro and in vivo

The overuse of antibiotics has led to the rapid development of multi-drug resistant bacteria, making antibiotics increasingly ineffective against bacterial infections. Consequently, there is an urgent need to develop alternative strategies to combat multi-drug-resistant bacterial infections. In this study, gold nanoparticles modified with ellagic acid (EA-AuNPs) were prepared using a simple and mild one-pot hydrothermal process. EA-AuNPs demonstrated high bactericidal efficacy and broad-spectrum antimicrobial activities against clinical isolates of the antibiotic-resistant ESKAPE pathogens. Furthermore, EA-AuNPs effectively disperse biofilms of multi-drug-resistant bacteria. Additionally, EA-AuNPs mitigated inflammatory responses at the bacterial infection sites. The combined bactericidal and anti-inflammatory treatment with EA-AuNPs resulted in faster curing of peritonitis caused by Staphylococcus aureus in mice compared to treatment with free EA or gentamicin. Moreover, transcriptome analysis revealed that EA-AuNPs exhibited a multi-targeting mechanism, making resistance development in pathogens more challenging than traditional antibiotics that recognize specific cellular targets. Overall, EA-AuNPs emerged as a promising antimicrobial agent against multi-drug-resistant bacterial infections.

A Lincomycin-Specific Antibody Was Developed Using Hapten Prediction, and an Immunoassay Was Established to Detect Lincomycin in Pork and Milk

Prolonged consumption of animal-derived foods containing high levels of lincomycin (LIN) residues can adversely impact human health. Therefore, it is essential to develop specific antibodies and immunoassay methods for LIN. This study utilized computational chemistry to predict the efficacy of LIN haptens prior to chemical synthesis, with subsequent confirmation obtained through an immunization experiment. A hybridoma cell line named LIN/1B11 was established, which is specific to LIN. The optimized indirect competitive enzyme-linked immunosorbent assay (ic-ELISA) method exhibited high specificity for detecting LIN residues, with an IC50 value of 0.57 ± 0.03 µg/kg. The method effectively detected LIN residues in pork and milk samples, achieving a limit of detection (LOD) ranging from 0.81 to 1.20 µg/kg and a limit of quantification (LOQ) ranging from 2.09 to 2.29 µg/kg, with recovery rates between 81.9% and 108.8%. This study offers a valuable tool for identifying LIN residues in animal-derived food products. Furthermore, the efficient hapten prediction method presented herein improves antibody preparation efficiency and provides a simple method for researchers in screening haptens.

Chloramphenicol Interferes with 50S Ribosomal Subunit Maturation via Direct and Indirect Mechanisms

Chloramphenicol (CAM), a well-known broad-spectrum antibiotic, inhibits peptide bond formation in bacterial ribosomes. It has been reported to affect ribosome assembly mainly through disrupting the balance of ribosomal proteins. The present study investigates the multifaceted effects of CAM on the maturation of the 50S ribosomal subunit in Escherichia coli (E. coli). Using label-free quantitative mass spectrometry (LFQ-MS), we observed that CAM treatment also leads to the upregulation of assembly factors. Further cryo-electron microscopy (cryo-EM) analysis of the ribosomal precursors characterized the CAM-treatment-accumulated pre-50S intermediates. Heterogeneous reconstruction identified 26 distinct pre-50S intermediates, which were categorized into nine main states based on their structural features. Our structural analysis highlighted that CAM severely impedes the formation of the central protuberance (CP), H89, and H58 during 50S ribosomal subunit maturation. The ELISA assay further demonstrated the direct binding of CAM to the ribosomal precursors, suggesting that the interference with 50S maturation occurs through a combination of direct and indirect mechanisms. These findings provide new insights into the mechanism of the action of CAM and provide a foundation for a better understanding of the assembly landscapes of the ribosome.

RNA-Binding Small Molecules in Drug Discovery and Delivery: An Overview from Fundamentals

RNA molecules, similar to proteins, fold into complex structures to confer diverse functions in cells. The intertwining of functions with RNA structures offers a new therapeutic opportunity for small molecules to bind and manipulate disease-relevant RNA pathways, thus creating a therapeutic realm of RNA-binding small molecules. The ongoing interest in RNA targeting and subsequent screening campaigns have led to the identification of numerous compounds that can regulate RNAs from splicing, degradation to malfunctions, with therapeutic benefits for a variety of diseases. Moreover, along with the rise of RNA-based therapeutics, RNA-binding small molecules have expanded their application to the modification, regulation, and delivery of RNA drugs, leading to the burgeoning interest in this field. This Perspective overviews the emerging roles of RNA-binding small molecules in drug discovery and delivery, covering aspects from their action fundamentals to therapeutic applications, which may inspire researchers to advance the field.

Berberine analog of chloramphenicol exhibits a distinct mode of action and unveils ribosome plasticity

Chloramphenicol (CHL) is an antibiotic targeting the peptidyl transferase center in bacterial ribosomes. We synthesized a new analog, CAM-BER, by substituting the dichloroacetyl moiety of CHL with a positively charged aromatic berberine group. CAM-BER suppresses bacterial cell growth, inhibits protein synthesis in vitro, and binds tightly to the 70S ribosome. Crystal structure analysis reveals that the bulky berberine group folds into the P site of the peptidyl transferase center (PTC), where it competes with the formyl-methionine residue of the initiator tRNA. Our toe-printing data confirm that CAM-BER acts as a translation initiation inhibitor in stark contrast to CHL, a translation elongation inhibitor. Moreover, CAM-BER induces a distinct rearrangement of conformationally restrained nucleotide A2059, suggesting that the 23S rRNA plasticity is significantly higher than previously thought. CAM-BER shows potential in avoiding CHL resistance and presents opportunities for developing novel berberine derivatives of CHL through medicinal chemistry exploration.

Stalled ribosome rescue factors exert different roles depending on types of antibiotics in Escherichia coli

Escherichia coli possesses three stalled-ribosome rescue factors, tmRNA·SmpB (primary factor), ArfA (alternative factor to tmRNA·SmpB), and ArfB. Here, we examined the susceptibility of rescue factor-deficient strains from E. coli SE15 to various ribosome-targeting antibiotics. Aminoglycosides specifically decreased the growth of the ΔssrA (tmRNA gene) strain, in which the levels of reactive oxygen species were elevated. The decrease in growth of ΔssrA could not be complemented by plasmid-borne expression of arfA, arfB, or ssrAAA to DD mutant gene possessing a proteolysis-resistant tag sequence. These results highlight the significance of tmRNA·SmpB-mediated proteolysis during growth under aminoglycoside stress. In contrast, tetracyclines or amphenicols decreased the growth of the ΔarfA strain despite the presence of tmRNA·SmpB. Quantitative RT-PCR revealed that tetracyclines and amphenicols, but not aminoglycosides, considerably induced mRNA expression of arfA. These findings indicate that tmRNA·SmpB, and ArfA exert differing functions during stalled-ribosome rescue depending on the type of ribosome-targeting antibiotic.

A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome

The global antibiotic resistance problem necessitates fast and effective approaches to finding novel inhibitors to treat bacterial infections. In this study, we propose a computational workflow to identify plausible high-affinity compounds from FDA-approved, investigational, and experimental libraries for the decoding center on the small subunit 30S of the E. coli ribosome. The workflow basically consists of two molecular docking calculations on the intact 30S, followed by molecular dynamics (MD) simulations coupled with MM-GBSA calculations on a truncated ribosome structure. The parameters used in the molecular docking suits, Glide and AutoDock Vina, as well as in the MD simulations with Desmond were carefully adjusted to obtain expected interactions for the ligand-rRNA complexes. A filtering procedure was followed, considering a fingerprint based on aminoglycoside's binding site on the 30S to obtain seven hit compounds either with different clinical usages or aminoglycoside derivatives under investigation, suggested for in vitro studies. The detailed workflow developed in this study promises an effective and fast approach for the estimation of binding free energies of large protein-RNA and ligand complexes.

Cell-Free Systems: Ideal Platforms for Accelerating the Discovery and Production of Peptide-Based Antibiotics

Peptide-based antibiotics (PBAs), including antimicrobial peptides (AMPs) and their synthetic mimics, have received significant interest due to their diverse and unique bioactivities. The integration of high-throughput sequencing and bioinformatics tools has dramatically enhanced the discovery of enzymes, allowing researchers to identify specific genes and metabolic pathways responsible for producing novel PBAs more precisely. Cell-free systems (CFSs) that allow precise control over transcription and translation in vitro are being adapted, which accelerate the identification, characterization, selection, and production of novel PBAs. Furthermore, these platforms offer an ideal solution for overcoming the limitations of small-molecule antibiotics, which often lack efficacy against a broad spectrum of pathogens and contribute to the development of antibiotic resistance. In this review, we highlight recent examples of how CFSs streamline these processes while expanding our ability to access new antimicrobial agents that are effective against antibiotic-resistant infections.

Medium-sized peptides from microbial sources with potential for antibacterial drug development

Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.

Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of elongation factor Tu or slowing translation elongation with chloramphenicol suppress the effects of G4 stabilization. In contrast, reducing expression of certain translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our integrated systems approach allowed us to propose a model for how RNA G4s can present barriers to E. coli growth and that reducing the rate of translation can compensate for G4-related stress.

Mechanism-guided strategies for combating antibiotic resistance

Bacterial antibiotic resistance has been recognized as a global threat to public health. It challenges the antibiotics currently used in clinical practice and causes severe and often fatal infectious diseases. Fighting against antibiotic-resistant bacteria (ARB) is growing more urgent. While understanding the molecular mechanisms that underlie resistance is a prerequisite, several major mechanisms have been previously proposed including bacterial efflux systems, reduced cell membrane permeability, antibiotic inactivation by enzymes, target modification, and target protection. In this context, this review presents a panel of promising and potential strategies to combat antibiotic resistance/resistant bacteria. Different types of direct-acting and indirect resistance breakers, such as efflux pump inhibitors, antibiotic adjuvants, and oxidative treatments are discussed. In addition, the emerging multi-omics approaches for rapid resistance identification and promising alternatives to existing antibiotics are highlighted. Overall, this review suggests that continued effort and investment in research are required to develop new antibiotics and alternatives to existing antibiotics and translate them into environmental and clinical applications.