Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design

Evaluating the innovative potential of the global antibacterial pipeline

BACKGROUND

Resistance burden varies widely among WHO regions, and the potential impact of new antibiotics differs in addressing the WHO's critical priority pathogens' resistance challenge.

OBJECTIVES

To analyse the current global clinical pipeline in line with public and global health concerns and define innovation in antibacterial drug discovery.

SOURCES

Monitoring clinical pipelines since 2006, integrating peer-reviewed MEDLINE publications on clinical development of new antibacterial agents, supplemented with disclosed data from developers.

CONTENT

The current clinical pipeline is dominated by derivatives of established antibiotic classes, primarily β-lactamase inhibitor combinations in Phase 3 (six of ten which also include two beta-lactams without β-lactamase inhibitor). This pattern extends to Phase 1. Although incremental improvements in susceptibility rates among derivatives benefit patients in advanced health care systems within specific geographical regions, these concepts are not adequate for carbapenem-resistant strains of Enterobacterales (especially Klebsiella and Escherichia coli), Acinetobacter, and Pseudomonas. This limitation arises from the diverse distribution of resistance mechanisms across global regions. Innovation in this context refers to absence of cross-resistance because of class-specific resistance mechanisms. This can most likely be achieved by exploring new chemical classes and new targets/binding sites, and new mode of action. An initial glimpse of progress is evident as innovative agents progressed to Phase 1 clinical trials. However, an influx of more agents advancing to clinical development is essential given the inherent risks associated with novel chemistry and targets.

IMPLICATIONS

The limited innovation in the global clinical pipeline inadequately serves public and global health interests. The complexities of antibacterial drug discovery, from scientific challenges to financial constraints, underscore the need for collective researcher efforts and public support to drive innovation for patients globally.

Structural basis for hygromycin B inhibition of yeast pseudouridine-deficient ribosomes

Eukaryotic ribosomes are enriched with pseudouridine, particularly at the functional centers targeted by antibiotics. Here, we investigated the roles of pseudouridine in aminoglycoside-mediated translation inhibition by comparing the structural and functional properties of the yeast wild-type and the pseudouridine-free ribosomes. We showed that the pseudouridine-free ribosomes have decreased thermostability and high sensitivity to aminoglycosides. When presented with a model internal ribosomal entry site RNA, elongation factor eEF2, GTP (guanosine triphosphate), and sordarin, hygromycin B preferentially binds to the pseudouridine-free ribosomes during initiation by blocking eEF2 binding, stalling ribosomes in a nonrotated conformation. The structures captured hygromycin B bound at the intersubunit bridge B2a enriched with pseudouridine and a deformed codon-anticodon duplex, revealing a functional link between pseudouridine and aminoglycoside inhibition. Our results suggest that pseudouridine enhances both thermostability and conformational fitness of the ribosomes, thereby influencing their susceptibility to aminoglycosides.

Long-term imaging of individual ribosomes reveals ribosome cooperativity in mRNA translation

The genetic information stored in mRNAs is decoded by ribosomes during mRNA translation. mRNAs are typically translated by multiple ribosomes simultaneously, but it is unclear whether and how the activity of different ribosomes on an mRNA is coordinated. Here, we develop an imaging approach based on stopless-ORF circular RNAs (socRNAs) to monitor translation of individual ribosomes in either monosomes or polysomes with very high resolution. Using experiments and simulations, we find that translating ribosomes frequently undergo transient collisions. However, unlike persistent collisions, such transient collisions escape detection by cellular quality control pathways. Rather, transient ribosome collisions promote productive translation by reducing ribosome pausing on problematic sequences, a process we term ribosome cooperativity. Ribosome cooperativity also reduces recycling of ribosomes by quality control pathways, thus enhancing processive translation. Together, our single-ribosome imaging approach reveals that ribosomes cooperate during translation to ensure fast and efficient translation.

Antibacterial and antibiofilm activities and mechanisms of Toona sinensis extracts against Bacillus cereus and its application in milk

Bacillus cereus, a well-known foodborne pathogen, poses an increased risk because of its ability to form biofilms. In this study, we evaluated the antibacterial and antibiofilm activities of Toona sinensis extracts against B. cereus. All tested T. sinensis varieties demonstrated significant antibacterial activity against B. cereus, with inhibition zone diameters exceeding 11 mm (P < 0.05). Notably, the extracts from Sichuan Dazhu exhibited strong antibacterial effects, even against antibiotic-resistant B. cereus strains. 239 compounds were identified in Sichuan Dazhu extracts by LC-MS. The MIC and MBC of the extracts against strain ATCC 11778, BCL043 and BCL047 were 0.195 and 0.391 mg/mL, respectively. These findings were corroborated by growth curve experiments, live/dead cell staining, and scanning electron microscopy observations. Moreover, the extracts demonstrated remarkable antibiofilm activity against B. cereus, reducing biofilm biomass to less than 40 % (P < 0.05). Transcriptome analysis revealed its antibacterial and antibiofilm mechanisms. Additionally, the extracts exhibited potent antibacterial activity against B. cereus in skim milk. Collectively, these results underscore the significant antibacterial and antibiofilm potential of T. sinensis extracts, highlighting their potential applications in food safety. This report provides the first evidence of both antibacterial and antibiofilm activities in T. sinensis extract against B. cereus, while also elucidating the associated mechanisms.

Novel nanomaterials-based combating strategies against drug-resistant bacteria

Numerous types of contemporary antibiotic treatment regimens have become ineffective with the increasing incidence of drug tolerance. As a result, it is pertinent to seek novel and innovative solutions such as antibacterial nanomaterials (NMs) for the prohibition and treatment of hazardous microbial infections. Unlike traditional antibiotics (e.g., penicillin and tetracycline), the unique physicochemical characteristics (e.g., size dependency) of NMs endow them with bacteriostatic and bactericidal potential. However, it is yet difficult to mechanistically predict or decipher the networks of molecular interaction (e.g., between NMs and the biological systems) and the subsequent immune responses. In light of such research gap, this review outlines various mechanisms accountable for the inception of drug tolerance in bacteria. It also delineates the primary factors governing the NMs-induced molecular mechanisms against microbes, specifically drug-resistant bacteria along with the various NM-based mechanisms of antibacterial activity. The review also explores future directions and prospects for NMs in combating drug-resistant bacteria, while addressing challenges to their commercial viability within the healthcare industry.

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome

Lasso peptides (biologically active molecules with a distinct structurally constrained knotted fold) are natural products that belong to the class of ribosomally synthesized and post-translationally modified peptides1-3. Lasso peptides act on several bacterial targets4,5, but none have been reported to inhibit the ribosome, one of the main targets of antibiotics in the bacterial cell6,7. Here we report the identification and characterization of the lasso peptide antibiotic lariocidin and its internally cyclized derivative lariocidin B, produced by Paenibacillus sp. M2, which has broad-spectrum activity against a range of bacterial pathogens. We show that lariocidins inhibit bacterial growth by binding to the ribosome and interfering with protein synthesis. Structural, genetic and biochemical data show that lariocidins bind at a unique site in the small ribosomal subunit, where they interact with the 16S ribosomal RNA and aminoacyl-tRNA, inhibiting translocation and inducing miscoding. Lariocidin is unaffected by common resistance mechanisms, has a low propensity for generating spontaneous resistance, shows no toxicity to human cells, and has potent in vivo activity in a mouse model of Acinetobacter baumannii infection. Our identification of ribosome-targeting lasso peptides uncovers new routes towards the discovery of alternative protein-synthesis inhibitors and offers a novel chemical scaffold for the development of much-needed antibacterial drugs.

Proteomic Analysis Reveals the Phenotypic Heterogeneity and Tolerance Mechanisms of Halophilic Vibrio parahaemolyticus Under Dual Stress of Low Salinity and Bile Salts in the Human Intestine

Vibrio parahaemolyticus, a halophilic Gram-negative bacterium commonly found in aquatic products, can colonize the human small intestine, causing gastroenteritis and potentially leukemia. As a major intestinal pathogen, it poses a significant threat to public health. This study aims to investigate the phenotypic heterogeneity of V. parahaemolyticus in the low-salinity and bile salt environments of the human intestinal tract and to elucidate its mechanisms of tolerance and pathogenicity using proteomics. The experimental results indicated that under the low salinity and bile salts conditions of the human intestinal environment, the growth, motility, and biofilm formation of the strains were significantly inhibited. Proteomics analysis revealed that, under these conditions, the energy metabolism, chemotaxis system, flagellar motor, and ribosome-related proteins of V. parahaemolyticus were significantly affected, thereby influencing its growth, motility, and biofilm formation. Furthermore, the activation of the secretion system, particularly the T2SS, enhanced the virulence of secreted factors on host cells. Additionally, the activation of the β-lactam resistance pathway increased resistance to the intestinal environment, thereby enhancing the pathogenicity of V. parahaemolyticus.

Global health perspectives on antibacterial drug discovery and the preclinical pipeline

Antibacterial resistance is a global challenge that requires a coordinated international response. The current clinical pipeline largely consists of derivatives of established antibiotic classes, whereas the discovery and preclinical pipeline is diverse and innovative including new direct-acting agents with no cross-resistance with existing antibiotics. These novel compounds target pathways such as lipoprotein synthesis, lipopolysaccharide biosynthesis and transport, outer membrane assembly, peptidoglycan biosynthesis, fatty acid biosynthesis and isoprenoid biosynthesis. If these agents can be developed into safe, effective and affordable drugs, they could address a broad range of infections worldwide, benefiting large patient populations without geographical limitations. However, strategies such as indirect-acting or pathogen-specific treatments are likely to benefit small patient groups, primarily in high-income countries that have advanced health-care systems and diagnostic infrastructure. Although encouraging, the discovery and preclinical pipeline remains insufficiently robust to offset the high attrition rates typical of early-stage drug innovation and to meet global health needs.

Mechanism of antibacterial and antibiofilm of thiazolidinone derivative TD-H2-A against Staphylococcus aureus

Staphylococcus aureus is one of the most common pathogens causing widespread infections. It has been demonstrated that thiazolidinone derivative (TD-H2-A), a small molecule compound that targets WalK protein through high-throughput screening, exerts antibacterial and anti-biofilm effects on S. aureus. In this study, we further ascertained the impact of TD-H2-A on biofilms at different stages. The phosphorylation assay and RNA sequencing were carried out to elucidate the underlying mechanism. The results revealed that TD-H2-A inhibited WalK autophosphorylation, implying that the antibacterial effect of TD-H2-A may be achieved by inhibiting the activity of WalK. The transcriptome analysis showed that TD-H2-A treatment induced 994 differentially expressed genes (DEGs), of which, 481 were upregulated and 513 were downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that 43 among 58 genes involved in ribosome synthesis were upregulated, and the transcript levels of the genes responsible for membrane transport were altered significantly. According to our research, TD-H2-A has an antibacterial mechanism with multitarget and multipathway. This study provided new ideas for the development of new drug target screening against S. aureus infections.

A plant peptide with dual activity against multidrug-resistant bacterial and fungal pathogens

Multidrug-resistant (MDR) bacteria pose a major threat to public health, and additional sources of antibacterial candidates are urgently needed. Noncanonical peptides (NCPs), derived from noncanonical small open reading frames, represent small biological molecules with important roles in biology. However, the antibacterial activity of NCPs remains largely unknown. Here, we discovered a plant-derived noncanonical antibacterial peptide (NCBP1) against both Gram-positive and Gram-negative bacteria. NCBP1 is composed of 11 amino acid residues with cationic surface potential and favorable safety and stability. Mechanistic studies revealed that NCBP1 displayed antibacterial activity by targeting phosphatidylglycerol and cardiolipin in bacterial membrane, resulting in membrane damage and dysfunction. Notably, NCBP1 showed promising efficacy in mice. Furthermore, NCBP1 effectively inhibited the growth of plant fungal pathogens and enhanced disease resistance in maize. Our results demonstrate the unexplored antimicrobial potential of plant-derived NCPs and provide an accessible source for the discovery of antimicrobial substances against MDR bacterial and fungal pathogens.

DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning

Ribonucleic Acid (RNA) is the central conduit for information transfer in the cell. Identifying potential RNA targets in disease conditions is a challenging task, given the vast repertoire of functional non-coding RNAs in a human cell. A potential druggable target must satisfy several criteria, including disease association, cellular accessibility, binding pockets for drug-like molecules, and minimal cross-reactivity. While several methods exist for prediction of druggable proteins, they cannot be repurposed for RNAs due to fundamental differences in their binding modality. Taking all these constraints into account, a new structure-based model, Druggable RNA-Ligand binding Pocket Selector (DRLiPS), is developed here to predict binding site-level druggability of any given RNA target. A novel strategy for sampling negative binding sites in RNA structures using three parallel approaches is demonstrated here to improve model specificity: backbone motif search, exhaustive pocket prediction, and blind docking. An external blind test dataset has also been curated to showcase the model's generalizability to both experimental and modelled apo state RNA structures. DRLiPS has achieved an F1-score of 0.70, precision of 0.61, specificity of 0.89, and recall of 0.73 on this external test dataset, outperforming two existing methods, DrugPred_RNA and RNACavityMiner. Further analysis indicates that the features selected for model-building generalize well to both apo and holo states with a backbone RMSD tolerance of 3 Å. It can also predict the effect of binding site single point mutations on druggability, which can aid in optimizing synthetic RNA aptamers for small molecule recognition. The DRLiPS model is freely accessible at https://web.iitm.ac.in/bioinfo2/DRLiPS/.

A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism

Protein synthesis by ribosomes produces functional proteins but also serves diverse regulatory functions, which depend on the coding amino acid sequences. Certain nascent peptides interact with the ribosome exit tunnel to arrest translation and modulate themselves or the expression of downstream genes. However, a comprehensive understanding of the mechanisms of such ribosome stalling and its regulation remains elusive. In this study, we systematically screen for unidentified ribosome arrest peptides through phenotypic evaluation, proteomics, and mass spectrometry analyses, leading to the discovery of the arrest peptides PepNL and NanCL in E. coli. Our cryo-EM study on PepNL reveals a distinct arrest mechanism, in which the N-terminus of PepNL folds back towards the tunnel entrance to prevent the catalytic GGQ motif of the release factor from accessing the peptidyl transferase center, causing translation arrest at the UGA stop codon. Furthermore, unlike sensory arrest peptides that require an arrest inducer, PepNL uses tryptophan as an arrest inhibitor, where Trp-tRNATrp reads through the stop codon. Our findings illuminate the mechanism and regulatory framework of nascent peptide-induced translation arrest, paving the way for exploring regulatory nascent peptides.

Creation of a macrolide antibiotic against non-tuberculous Mycobacterium using late-stage boron-mediated aglycon delivery

Non-tuberculous mycobacteria (NTM) is gaining clinical recognition as a recently emerging pulmonary pathogen. Mycobacterium avium complex (MAC), the most common NTM, is the cause of pulmonary MAC disease. Currently, the macrolide azithromycin (AZM) is the standard first-line antibiotic for treatment of the disease. However, the rise of drug-resistant MAC necessitates the development of alternative therapeutics. Here, we present a late-stage boron-mediated aglycon delivery strategy for selective modification of AZM, generating a library of potential anti-MAC drugs designated KU01 to KU13. Screening of KU01 to KU13 revealed that KU13 exhibited enhanced antimicrobial activity against wild-type and macrolide-resistant MAC compared to AZM. Cryo-electron microscopy analysis indicated that the inserted tercyclic moiety of KU13 formed a robust anchor on the bacterial ribosome, creating a binding pocket with base flipping of U2847, potentially bypassing the standard mechanism of macrolide resistance. These results position KU13 as a promising lead for therapeutics against macrolide-resistant MAC.

Impacts of ribosomal RNA sequence variation on gene expression and phenotype

Since the framing of the Central Dogma, it has been speculated that physically distinct ribosomes within cells may influence gene expression and cellular physiology. While heterogeneity in ribosome composition has been reported in bacteria, protozoans, fungi, zebrafish, mice and humans, its functional implications remain actively debated. Here, we review recent evidence demonstrating that expression of conserved variant ribosomal DNA (rDNA) alleles in bacteria, mice and humans renders their actively translating ribosome pool intrinsically heterogeneous at the level of ribosomal RNA (rRNA). In this context, we discuss reports that nutrient limitation-induced stress in Escherichia coli leads to changes in variant rRNA allele expression, programmatically altering transcription and cellular phenotype. We highlight that cells expressing ribosomes from distinct operons exhibit distinct drug sensitivities, which can be recapitulated in vitro and potentially rationalized by subtle perturbations in ribosome structure or in their dynamic properties. Finally, we discuss evidence that differential expression of variant rDNA alleles results in different populations of ribosome subtypes within mammalian tissues. These findings motivate further research into the impacts of rRNA heterogeneities on ribosomal function and predict that strategies targeting distinct ribosome subtypes may hold therapeutic potential.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.

Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research

In the fight against bacterial infections, particularly those caused by multi-resistant pathogens known as "superbugs", the need for new antibacterials is undoubted in scientific communities and is by now also widely perceived by the general population. However, the antibacterial research landscape has changed considerably over the past years. With few exceptions, the majority of big pharma companies has left the field and thus, the decline in R&D on antibacterials severely impacts the drug pipeline. In recent years, antibacterial research has increasingly relied on smaller companies or academic research institutions, which mostly have only limited financial resources, to carry a drug discovery and development process from the beginning and through to the beginning of clinical phases. This review formulates the requirements for an antibacterial in regard of targeted pathogens, resistance mechanisms and drug discovery. Strategies are shown for the discovery of new antibacterial structures originating from natural sources, by chemical synthesis and more recently from artificial intelligence approaches. This is complemented by principles for the computer-aided design of antibacterials and the refinement of a lead structure. The second part of the article comprises a compilation of antibacterial molecules classified according to bacterial target structures, e.g. cell wall synthesis, protein synthesis, as well as more recently emerging target classes, e.g. fatty acid synthesis, proteases and membrane proteins. Aspects of the origin, the antibacterial spectrum, resistance and the current development status of the presented drug molecules are highlighted.

Tumor-Resident Intracellular Bacteria Scavenger Activated In Situ Vaccines for Potent Cancer Photoimmunotherapy

In situ tumor vaccines, which utilize antigens generated during tumor treatment to stimulate a cancer patient's immune system, has become a potential field in cancer immunotherapy. However, due to the immunosuppressive tumor microenvironment (ITME), the generation of tumor antigens is always mild and not sufficient. Tumor-resident intracellular bacteria have been identified as a complete tumor microenvironment component to contribute to creating ITME. Herein, a tumor-resident intracellular bacteria scavenger is designed to induce enhanced antitumor photoimmunotherapy-driven in situ vaccines for treating hypoxic tumors. This scavenger is developed by integrating photosensitizer CyI and antibiotics Doxycycline (Doxy) into thermal-sensitive tumor-derived exosomes fused liposomes (ECDL). In vitro and in vivo results showed that ECDL could homologous target to cancer cells and restrict the respiration of mitochondrial to reduce tumor hypoxia, thus providing continuous oxygen to eliminate both tumor cells and tumor-resident intracellular bacteria, which could induce in situ vaccines for ablating the primary tumor and inhibiting the tumor metastasis and recurrence. Moreover, eliminating tumor-resident intracellular bacteria neutralizes the ITME and triggers the production of bacterial-related neoantigens, which could further strength the immunotherapy. This study provided versatile and effective in situ vaccines that are promising for local, abscopal, and metastatic tumor treatment.

Co-translational protein aggregation and ribosome stalling as a broad-spectrum antibacterial mechanism

Drug-resistant bacteria pose an urgent global health threat, necessitating the development of antibacterial compounds with novel modes of action. Protein biosynthesis accounts for up to half of the energy expenditure of bacterial cells, and consequently inhibiting the efficiency or fidelity of the bacterial ribosome is a major target of existing antibiotics. Here, we describe an alternative mode of action that affects the same process: allowing translation to proceed but causing co-translational aggregation of the nascent peptidic chain. We show that treatment with an aggregation-prone peptide induces formation of polar inclusion bodies and activates the SsrA ribosome rescue pathway in bacteria. The inclusion bodies contain ribosomal proteins and ribosome hibernation factors, as well as mRNAs and cognate nascent chains of many proteins in amyloid-like structures, with a bias for membrane proteins with a fold rich in long-range beta-sheet interactions. The peptide is bactericidal against a wide range of pathogenic bacteria in planktonic growth and in biofilms, and reduces bacterial loads in mouse models of Escherichia coli and Acinetobacter baumannii infections. Our results indicate that disrupting protein homeostasis via co-translational aggregation constitutes a promising strategy for development of broad-spectrum antibacterials.

Molecular pathogenesis of Cryptosporidium and advancements in therapeutic interventions

Cryptosporidiosis, caused by a Cryptosporidium infection, is a serious gastrointestinal disease commonly leading to diarrhea in humans. This disease poses a particular threat to infants, young children, and those with weakened immune systems. The treatment of cryptosporidiosis is challenging due to the current lack of an effective treatment or vaccine. Ongoing research is focused on understanding the molecular pathogenesis of Cryptosporidium and developing pharmacological treatments. In this review, we examine the signaling pathways activated by Cryptosporidium infection within the host and their role in protecting host epithelial cells. Additionally, we also review the research progress of chemotherapeutic targets against cryptosporidia-specific enzymes and anti-Cryptosporidium drugs (including Chinese and Western medicinal drugs), aiming at the development of more effective treatments for cryptosporidiosis.

Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells

Ribosome-targeting antibiotics represent an important class of antimicrobial drugs. Chloramphenicol (Cm) is a well-studied ribosomal peptidyl transferase center (PTC) binder and growing evidence suggests that its inhibitory action depends on the sequence of the nascent peptide. How such selective inhibition on the molecular scale manifests on the cellular level remains unclear. Here, we use cryo-electron tomography to analyze the impact of Cm inside the bacterium Mycoplasma pneumoniae. By resolving the Cm-bound ribosomes to 3.0 Å, we elucidate Cm's coordination with natural nascent peptides and transfer RNAs in the PTC. We find that Cm leads to the accumulation of a number of translation elongation states, indicating ongoing futile accommodation cycles, and to extensive ribosome collisions. We, thus, suggest that, beyond its direct inhibition of protein synthesis, the action of Cm may involve the activation of cellular stress responses. This work exemplifies how in-cell structural biology can expand the understanding of mechanisms of action for extensively studied antibiotics.

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.

Chloramphenicol and gentamicin reduce the evolution of resistance to phage ΦX174 by suppressing a subset of E. coli LPS mutants

Bacteriophages infect gram-negative bacteria by attaching to molecules present on the bacterial surface, often lipopolysaccharides (LPS). Modification of LPS can lead to resistance to phage infection. In addition, LPS modifications can impact antibiotic susceptibility, allowing for phage-antibiotic synergism. The evolutionary mechanism(s) behind such synergistic interactions remain largely unclear. Here, we show that the presence of antibiotics can affect the evolution of resistance to phage infection, using phage ΦX174 and Escherichia coli C. We use a collection of 34 E. coli C LPS strains, each of which is resistant to ΦX174, and has either a "rough" or "deep rough" LPS phenotype. Growth of the bacterial strains with the deep rough phenotype is inhibited at low concentrations of chloramphenicol and, to a much lesser degree, gentamicin. Treating E. coli C wild type with ΦX174 and chloramphenicol eliminates the emergence of mutants with the deep rough phenotype, and thereby slows the evolution of resistance to phage infection. At slightly lower chloramphenicol concentrations, phage resistance rates are similar to those observed at high concentrations; yet, we show that the diversity of possible mutants is much larger than at higher chloramphenicol concentrations. These data suggest that specific antibiotic concentrations can lead to synergistic phage-antibiotic interactions that disappear at higher antibiotic concentrations. Overall, we show that the change in survival of various ΦX174-resistant E. coli C mutants in the presence of antibiotics can explain the observed phage-antibiotic synergism.

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.

Niacin-Cholic Acid-Peptide Conjugate Act as a Potential Antibiotic Adjuvant to Mitigate Polymicrobial Infections Caused by Gram-Negative Pathogens

Polymicrobial wound infections caused by Gram-negative bacteria and associated inflammation are challenging to manage, as many antibiotics do not work against these infections. Utilizing adjuvants to repurpose the existing antibiotics for mitigating microbial infections presents an alternative therapeutic strategy. We designed and developed a niacin-cholic acid-peptide conjugate (1) to rejuvenate the therapeutic efficacy of macrolide antibiotics against Gram-negative pathogens. We conjugated niacin with anti-inflammatory properties at the carboxyl terminal of the cholic acid and dipeptide (glycine-valine) at the three hydroxyl terminals of cholic acid to obtain the amphiphile 1. Our findings demonstrated that amphiphile 1 serves as a microbial membrane disruptor that facilitates the entry of erythromycin (ERY) in bacterial cells. The combination of amphiphile 1 and ERY is bactericidal and can effectively eliminate monomicrobial and polymicrobial Gram-negative bacterial biofilms. We further demonstrated the antibacterial effectiveness of combining 1 and ERY against monomicrobial and polymicrobial wound infections. Together, these findings indicate that amphiphile 1 revitalizes the remedial efficacy of ERY against Gram-negative bacteria.

Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms

Growing resistance toward ribosome-targeting macrolide antibiotics has limited their clinical utility and urged the search for superior compounds. Macrolones are synthetic macrolide derivatives with a quinolone side chain, structurally similar to DNA topoisomerase-targeting fluoroquinolones. While macrolones show enhanced activity, their modes of action have remained unknown. Here, we present the first structures of ribosome-bound macrolones, showing that the macrolide part occupies the macrolide-binding site in the ribosomal exit tunnel, whereas the quinolone moiety establishes new interactions with the tunnel. Macrolones efficiently inhibit both the ribosome and DNA topoisomerase in vitro. However, in the cell, they target either the ribosome or DNA gyrase or concurrently both of them. In contrast to macrolide or fluoroquinolone antibiotics alone, dual-targeting macrolones are less prone to select resistant bacteria carrying target-site mutations or to activate inducible macrolide resistance genes. Furthermore, because some macrolones engage Erm-modified ribosomes, they retain activity even against strains with constitutive erm resistance genes.

Transcriptome and interactome-based analyses to unravel crucial proteins and pathways involved in Acinetobacter baumannii pathogenesis

The present study employed an integrated transcriptome and interactome-based analyses to identify key proteins and pathways associated with Acinetobacter baumannii infection towards the development of novel therapeutics against this pathogen. Transcriptome analysis of A.baumannii strains (ATCC 17978 and AbH12O-A2) identified 253 and 619 differentially expressed genes (DEGs), respectively. These genes were involved in essential molecular functions, including DNA binding, metal ion binding, and oxidoreductase activity. The centrality and module analyses of these identified DEGs had shortlisted 27 and 41 hub proteins, which were central to the ATCC 17978 and AbH12O-A2 networks, and essential for bacterial survival. Significantly, three proteins (SecA, glutathione synthase, and aromatic-amino-acid transaminase) from the ATCC 17978 strain and seven proteins (ATP synthase subunit alpha, translation initiation factor IF-2, SecY, elongation factors G, Tu, and Ts, and tRNA guanine-N1-methyltransferase) from the AbH12O-A2 strain showed interactions with human proteins, identified through host-pathogen interaction (HPI) analysis of hub proteins (referred as hub-HPI proteins). These proteins were observed to participate in vital pathways, including glutathione metabolism, secondary metabolite biosynthesis and quorum sensing. Targeting these hub-HPI proteins through novel therapeutic strategies holds the potential to disrupt the critical bacterial pathways, thereby controlling A. baumannii infections. Furthermore, their localization analysis indicated that nine proteins were cytoplasmic and one was membrane protein. Among them, six were druggable and four were novel proteins. Overall, this comprehensive study provides valuable insights into the crucial proteins and pathways involved during A. baumannii infection, and offers potential therapeutic targets for designing novel antimicrobial agents to tackle the pathogen.

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.

Recent advances and challenges of revolutionizing drug-resistant tuberculosis treatment

Tuberculosis (TB), an infectious disease induced by Mycobacterium tuberculosis, is one of the primary public health threats all over the world. Since the prevalence of first-line anti-TB agents, the morbidity and mortality issues of TB descended obviously. Nevertheless, the emergences of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains, the double prevalence of HIV-TB co-infection, and the insufficiency of plentiful health care have led to an increased incidence of TB. It is noted that current drugs for treating TB have proved unsustainable in the face of highly resistant strains. Fortunately, five categories of new drugs and candidates with new mechanisms of action have emerged in the field of anti-TB research after decades of stagnation in the progression of anti-TB drugs. In this paper, the research status of these promising anti-TB drugs and candidates are reviewed, emphasizing the challenges to be addressed for efficient development of future TB therapies.

Exploring synergistic and antagonistic interactions in phage-antibiotic combinations against ESKAPE pathogens

In the era of antimicrobial resistance, phage-antibiotic combinations offer a promising therapeutic option, yet research on their synergy and antagonism is limited. This study aims to assess these interactions, focusing on protein synthesis inhibitors and cell envelope-active agents against multidrug-resistant bacterial strains. We evaluated synergistic and antagonistic interactions in multidrug-resistant Staphylococcus aureus, Enterococcus faecium, and Pseudomonas aeruginosa strains. Phages were combined with protein synthesis inhibitors [linezolid (LZD), minocycline (MIN), gentamicin (GEN), and azithromycin (AZM)] or cell envelope-active agents [daptomycin (DAP), ceftaroline (CPT), and cefepime (FEP)]. Modified checkerboard minimum inhibitory concentration assays and 24-h time-kill analyses were conducted, alongside one-step growth curves to analyze phage growth kinetics. Statistical comparisons used one-way analysis of variance (ANOVA) and the Tukey test (P < 0.05). In the checkerboard and 24-h time-kill analyses (TKA) of S. aureus and E. faecium, phage-LZD and phage-MIN combinations were antagonistic (FIC > 4) while phage-DAP and phage-CPT were synergistic (FIC 0.5) (ANOVA range of mean differences 0.52-2.59 log10 CFU/mL; P < 0.001). For P. aeruginosa, phage-AZM was antagonistic (FIC > 4), phage-GEN was additive (FIC = 1), and phage-FEP was synergistic (ANOVA range of mean differences 1.04-1.95 log10 CFU/mL; P < 0.001). Phage growth kinetics were altered in the presence of LZD and MIN against S. aureus and in the presence of LZD against a single E. faecium strain (HOU503). Our findings indicate that select protein synthesis inhibitors may induce phage-antibiotic antagonism. However, this antagonism may not solely stem from changes in phage growth kinetics, warranting further investigation into the complex interplay among strains, phage attributes, and antibiotic mechanisms affecting bacterial inhibition.IMPORTANCEIn the face of escalating antimicrobial resistance, combining phages with antibiotics offers a promising avenue for treating infections unresponsive to traditional antibiotics. However, while studies have explored synergistic interactions, less attention has been given to potential antagonism and its impact on phage growth kinetics. This research evaluates the interplay between phages and antibiotics, revealing both synergistic and antagonistic patterns across various bacterial strains and shedding light on the complex dynamics that influence treatment efficacy. Understanding these interactions is crucial for optimizing combination therapies and advancing phage therapy as a viable solution for combating antimicrobial resistance.

Efficacy and safety of eravacycline (ERV) in treating infections caused by Gram-negative pathogens: a systematic review and meta-analysis

BACKGROUND

Eravacycline (ERV) is a novel synthetic fluorocycline antibiotic with broad-spectrum antibacterial efficacy against pathogens. This study sought to investigate ERV's effectiveness and safety in treating Gram-negative pathogens (GNPs) infections.

METHODS

We conducted a comprehensive search of PubMed, Cochrane Library, Embase, Web of Science, and ClinicalTrials.gov up to September 2023. Included in the review were studies assessing the efficacy or safety of ERV in treating GNP infections.

RESULTS

Three randomized controlled trials, seven cohort studies, and two case reports were included. There was no statistically significant difference between ERV and comparators in clinical cure (OR = 0.84, 95% CI = 0.59-1.19), microbiologic eradication (OR = 0.69, 95% CI = 0.36-1.33), and mortality (OR = 1.66, 95% CI = 0.81-3.41). However, a significantly higher rate of adverse events with ERV was observed compared to the control group (OR = 1.55, 95% CI = 1.21-1.99). Additionally, cohort studies reported a clinical cure rate of 73.2% (88.8% in RCTs), an AE rate of 4.5% (38.3% in RCTs), and mortality of 16.2% (1.5% in RCTs). Patients in RCTs received ERV monotherapy, whereas almost half of the patients in cohort studies were treated with ERV in combination with other antibiotics.

CONCLUSIONS

Further studies are warranted to investigate the safety and efficacy of ERV monotherapy or combination therapy in critically ill patients.

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.

Oxydifficidin, a potent Neisseria gonorrhoeae antibiotic due to DedA assisted uptake and ribosomal protein RplL sensitivity

Gonorrhea, which is caused by Neisseria gonorrhoeae, is the second most reported sexually transmitted infection worldwide. The increasing appearance of isolates that are resistant to approved therapeutics raises the concern that gonorrhea may become untreatable. Here, we serendipitously identified oxydifficidin as a potent N. gonorrhoeae antibiotic through the observation of a Bacillus amyloliquefaciens contaminant in a lawn of N. gonorrhoeae. Oxydifficidin is active against both wild-type and multidrug-resistant N. gonorrhoeae. It's potent activity results from a combination of DedA-assisted uptake into the cytoplasm and the presence of an oxydifficidin-sensitive ribosomal protein L7/L12 (RplL). Our data indicates that oxydifficidin binds to the ribosome at a site that is distinct from other antibiotics and that L7/L12 is uniquely associated with its mode of action. This study opens a potential new avenue for addressing antibiotic resistant gonorrhea and underscores the possibility of identifying overlooked natural products from cultured bacteria, particularly those with activity against previously understudied pathogens.

Unveil the Molecular Interplay between Aminoglycosides and Pseudouridine in IRES Translation

Eukaryotic ribosomes are enriched with pseudouridine, particularly at the functional centers targeted by antibiotics. Here we investigated the roles of pseudouridine in aminoglycoside-mediated translation inhibition by comparing the structural and functional properties of the wild-type ribosomes and those lacking pseudouridine ( cbf5 -D95A). We showed that the cbf5 -D95A ribosomes have decreased thermostability and high sensitivity to aminoglycosides. When presented with an internal ribosome entry site (IRES) RNA, elongation factor eEF2, GTP, sordarin, hygromycin B preferentially binds to the cbf5 -D95A ribosomes during initiation by blocking eEF2 binding and stalls the ribosomes in a non-rotated conformation, further hindering translocation. Hygromycin B binds to the inter-subunit bridge B2a that is known to be sensitive to pseudouridine, revealing a functional link between pseudouridine and aminoglycoside inhibition. Our results suggest that pseudouridine enhances both thermostability and conformational fitness of the ribosomes, thereby influencing their susceptibility to aminoglycosides.

Highlights

Loss of pseudouridine increases cell sensitivity to aminoglycosidesPseudouridine enhances ribosome thermostabilityHygromycin B competes with eEF2 for the non-rotated ribosomeHygromycin B deforms the codon-anticodon duplex.

A Broad Spectrum Lasso Peptide Antibiotic Targeting the Bacterial Ribosome

Lasso peptides, biologically active molecules with a distinct structurally constrained knotted fold, are natural products belonging to the class of ribosomally-synthesized and posttranslationally modified peptides (RiPPs). Lasso peptides act upon several bacterial targets, but none have been reported to inhibit the ribosome, one of the main antibiotic targets in the bacterial cell. Here, we report the identification and characterization of the lasso peptide antibiotic, lariocidin (LAR), and its internally cyclized derivative, lariocidin B (LAR-B), produced by Paenabacillussp. M2, with broad-spectrum activity against many bacterial pathogens. We show that lariocidins inhibit bacterial growth by binding to the ribosome and interfering with protein synthesis. Structural, genetic, and biochemical data show that lariocidins bind at a unique site in the small ribosomal subunit, where they interact with the 16S rRNA and aminoacyl-tRNA, inhibiting translocation and inducing miscoding. LAR is unaffected by common resistance mechanisms, has a low propensity for generating spontaneous resistance, shows no human cell toxicity, and has potent in vivo activity in a mouse model of Acinetobacter baumannii infection. Our finding of the first ribosome-targeting lasso peptides uncovers new routes toward discovering alternative protein synthesis inhibitors and offers a new chemical scaffold for developing much-needed antibacterial drugs.

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.

DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

Small-molecule compounds that elicit mRNA-selective translation repression have attracted interest due to their potential for expansion of druggable space. However, only a limited number of examples have been reported to date. Here, we show that desmethyl desamino pateamine A (DMDA-PatA) represses translation in an mRNA-selective manner by clamping eIF4A, a DEAD-box RNA-binding protein, onto GNG motifs. By systematically comparing multiple eIF4A inhibitors by ribosome profiling, we found that DMDA-PatA has unique mRNA selectivity for translation repression. Unbiased Bind-n-Seq reveals that DMDA-PatA-targeted eIF4A exhibits a preference for GNG motifs in an ATP-independent manner. This unusual RNA binding sterically hinders scanning by 40S ribosomes. A combination of classical molecular dynamics simulations and quantum chemical calculations, and the subsequent development of an inactive DMDA-PatA derivative reveals that the positive charge of the tertiary amine on the trienyl arm induces G selectivity. Moreover, we identified that DDX3, another DEAD-box protein, is an alternative DMDA-PatA target with the same effects on eIF4A. Our results provide an example of the sequence-selective anchoring of RNA-binding proteins and the mRNA-selective inhibition of protein synthesis by small-molecule compounds.

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.

SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening

The growing interest in RNA-targeted drugs underscores the need for computational modeling of interactions between RNA molecules and small compounds. Having a reliable scoring function for RNA-ligand interactions is essential for effective computational drug screening. An ideal scoring function should not only predict the native pose for ligand binding but also rank the affinity of the binding for different ligands. However, existing scoring functions are primarily designed to predict the native binding modes for a given RNA-ligand pair and have not been thoroughly assessed for virtual screening purposes. In this paper, we introduce SPRank, a combination of machine-learning and knowledge-based scoring functions developed through a weighted iterative approach, specifically designed to tackle both binding mode prediction and virtual screening challenges. Our approach incorporates third-party docking software, such as rDock and AutoDock Vina, to sample flexible ligands against an ensemble of RNA structures, capturing the conformational flexibility of both the RNA and the ligand. Through rigorous testing, SPRank demonstrates improved performance compared to the tested scoring functions across four test sets comprising 122, 42, 55, and 71 nucleic acid-ligand complexes. Furthermore, SPRank exhibits improved performance in virtual screening tests targeting the HIV-1 TAR ensemble, which highlights its advantage in drug discovery. These results underscore the advantages of SPRank as a potentially promising tool for the RNA-targeted drug design. The source code of SPRank and the data sets are freely accessible at https://github.com/Vfold-RNA/SPRank.

RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution

Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here, we find that a broad range of ribosome-targeting antibiotics cause mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we find that the translation inhibitor causes genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. Further analysis shows that the stalling is caused by the disruption of transcription-translation coupling. Anti-intuitively, the stalled RNAPs subsequently induce lesions to the DNA via transcription-coupled repair. While most of the bacteria are killed by genotoxicity, a small subpopulation acquires mutations via SOS-induced mutagenesis. Given that these processes are triggered shortly after antibiotic addition, resistance rapidly emerges in the population. Our work reveals a mechanism of action of ribosomal antibiotics, illustrates the importance of dissecting the complex interplay between multiple molecular processes in understanding antibiotic efficacy, and suggests new strategies for countering the development of resistance.

Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives

Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.

Antimicrobial activity of metal-based nanoparticles: a mini-review

The resistance of pathogenic microorganisms to antibiotics is one of the main problems of world health. Of particular concern are multidrug-resistant (MDR) bacteria. Infections caused by these microorganisms affect the appearance of acute or chronic diseases. In this regard, modern technologies, such as nanomaterials (NMs), especially promising nanoparticles (NPs), can possess antimicrobial properties or improve the effectiveness and delivery of known antibiotics. Their diversity and characteristics, combined with surface functionalization, enable multivalent interactions with microbial biomolecules. This article presents an overview of the most current research on replacing antibiotics with NPs, including the prospects and risks involved.

Hibernating ribosomes as drug targets?

When ribosome-targeting antibiotics attack actively growing bacteria, they occupy ribosomal active centers, causing the ribosomes to stall or make errors that either halt cellular growth or cause bacterial death. However, emerging research indicates that bacterial ribosomes spend a considerable amount of time in an inactive state known as ribosome hibernation, in which they dissociate from their substrates and bind to specialized proteins called ribosome hibernation factors. Since 60% of microbial biomass exists in a dormant state at any given time, these hibernation factors are likely the most common partners of ribosomes in bacterial cells. Furthermore, some hibernation factors occupy ribosomal drug-binding sites - leading to the question of how ribosome hibernation influences antibiotic efficacy, and vice versa. In this review, we summarize the current state of knowledge on physical and functional interactions between hibernation factors and ribosome-targeting antibiotics and explore the possibility of using antibiotics to target not only active but also hibernating ribosomes. Because ribosome hibernation empowers bacteria to withstand harsh conditions such as starvation, stress, and host immunity, this line of research holds promise for medicine, agriculture, and biotechnology: by learning to regulate ribosome hibernation, we could enhance our capacity to manage the survival of microorganisms in dormancy.

Synthetic macrolides overcoming MLSBK-resistant pathogens

Conventional macrolide-lincosamide-streptogramin B-ketolide (MLSBK) antibiotics are unable to counter the growing challenge of antibiotic resistance that is conferred by the constitutive methylation of rRNA base A2058 or its G2058 mutation, while the presence of unmodified A2058 is crucial for high selectivity of traditional MLSBK in targeting pathogens over human cells. The absence of effective modes of action reinforces the prevailing belief that constitutively antibiotic-resistant Staphylococcus aureus remains impervious to existing macrolides including telithromycin. Here, we report the design and synthesis of a novel series of macrolides, featuring the strategic fusion of ketolide and quinolone moieties. Our effort led to the discovery of two potent compounds, MCX-219 and MCX-190, demonstrating enhanced antibacterial efficacy against a broad spectrum of formidable pathogens, including A2058-methylated Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, and notably, the clinical Mycoplasma pneumoniae isolates harboring A2058G mutations which are implicated in the recent pneumonia outbreak in China. Mechanistic studies reveal that the modified quinolone moiety of MCX-190 establishes a distinctive secondary binding site within the nascent peptide exit tunnel. Structure-activity relationship analysis underscores the importance of this secondary binding, maintained by a sandwich-like π-π stacking interaction and a water-magnesium bridge, for effective engagement with A2058-methylated ribosomes rather than topoisomerases targeted by quinolone antibiotics. Our findings not only highlight MCX-219 and MCX-190 as promising candidates for next-generation MLSBK antibiotics to combat antibiotic resistance, but also pave the way for the future rational design of the class of MLSBK antibiotics, offering a strategic framework to overcome the challenges posed by escalating antibiotic resistance.

Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it

The bacterial ribosome is an essential drug target as many clinically important antibiotics bind and inhibit its functional centers. The catalytic peptidyl transferase center (PTC) is targeted by the broadest array of inhibitors belonging to several chemical classes. One of the most abundant and clinically prevalent resistance mechanisms to PTC-acting drugs in Gram-positive bacteria is C8-methylation of the universally conserved A2503 nucleobase by Cfr methylase in 23S ribosomal RNA. Despite its clinical importance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. Here, we report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-transfer RNAs. These structures reveal an allosteric rearrangement of nucleotide A2062 upon Cfr-mediated methylation of A2503 that likely contributes to the reduced potency of some PTC inhibitors. Additionally, we provide the structural bases behind two distinct mechanisms of engaging the Cfr-methylated ribosome by the antibiotics iboxamycin and tylosin.

The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center

Translation termination is an essential cellular process, which is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires eRF1, which recognizes stop codons, catalyzes the release of nascent proteins from ribosomes and facilitates ribosome recycling. The small molecule SRI-41315 triggers eRF1 degradation and enhances translational readthrough of premature stop codons. However, the mechanism of action of SRI-41315 on eRF1 and translation is not known. Here we report cryo-EM structures showing that SRI-41315 acts as a metal-dependent molecular glue between the N domain of eRF1 responsible for stop codon recognition and the ribosomal subunit interface near the decoding center. Retention of eRF1 on ribosomes by SRI-41315 leads to ribosome collisions, eRF1 ubiquitylation and a higher frequency of translation termination at near-cognate stop codons. Our findings reveal a new mechanism of release factor inhibition and additional implications for pharmacologically targeting eRF1.

Preserving the efficacy of antibiotics to tackle antibiotic resistance

Different international agencies recognize that antibiotic resistance is one of the most severe human health problems that humankind is facing. Traditionally, the introduction of new antibiotics solved this problem but various scientific and economic reasons have led to a shortage of novel antibiotics at the pipeline. This situation makes mandatory the implementation of approaches to preserve the efficacy of current antibiotics. The concept is not novel, but the only action taken for such preservation had been the 'prudent' use of antibiotics, trying to reduce the selection pressure by reducing the amount of antibiotics. However, even if antibiotics are used only when needed, this will be insufficient because resistance is the inescapable outcome of antibiotics' use. A deeper understanding of the alterations in the bacterial physiology upon acquisition of resistance and during infection will help to design improved strategies to treat bacterial infections. In this article, we discuss the interconnection between antibiotic resistance (and antibiotic activity) and bacterial metabolism, particularly in vivo, when bacteria are causing infection. We discuss as well how understanding evolutionary trade-offs, as collateral sensitivity, associated with the acquisition of resistance may help to define evolution-based therapeutic strategies to fight antibiotic resistance and to preserve currently used antibiotics.

Antibiotic resistance: A key microbial survival mechanism that threatens public health

Antibiotic resistance (AMR) is a global public health threat, challenging the effectiveness of antibiotics in combating bacterial infections. AMR also represents one of the most crucial survival traits evolved by bacteria. Antibiotics emerged hundreds of millions of years ago as advantageous secondary metabolites produced by microbes. Consequently, AMR is equally ancient and hardwired into the genetic fabric of bacteria. Human use of antibiotics for disease treatment has created selection pressure that spurs the evolution of new resistance mechanisms and the mobilization of existing ones through bacterial populations in the environment, animals, and humans. This integrated web of resistance elements is genetically complex and mechanistically diverse. Addressing this mode of bacterial survival requires innovation and investment to ensure continued use of antibiotics in the future. Strategies ranging from developing new therapies to applying artificial intelligence in monitoring AMR and discovering new drugs are being applied to manage the growing AMR crisis.

Inactivation of the ribosome assembly factor RimP causes streptomycin resistance and impairs motility in Salmonella

The ribosome is the central hub for protein synthesis and the target of many antibiotics. Although the majority of ribosome-targeting antibiotics inhibit protein synthesis and are bacteriostatic, aminoglycosides promote protein mistranslation and are bactericidal. Understanding the resistance mechanisms of bacteria against aminoglycosides is not only vital for improving the efficacy of this critically important group of antibiotics but also crucial for studying the molecular basis of translational fidelity. In this work, we analyzed Salmonella mutants evolved in the presence of the aminoglycoside streptomycin (Str) and identified a novel gene rimP to be involved in Str resistance. RimP is a ribosome assembly factor critical for the maturation of the 30S small subunit that binds Str. Deficiency in RimP increases resistance against Str and facilitates the development of even higher resistance. Deleting rimP decreases mistranslation and cellular uptake of Str and further impairs flagellar motility. Our work thus highlights a previously unknown mechanism of aminoglycoside resistance via defective ribosome assembly.

Differential effects of translation inhibitors on Plasmodium berghei liver stage parasites

Increasing numbers of antimalarial compounds are being identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of the molecular target or mechanism. A deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential could prove useful. Here, we probed that relationship using the Plasmodium berghei-HepG2 liver stage infection model. After determining translation inhibition EC50s for five compounds, we tested them at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, followed by parasites to 120 h post-infection to assess antiplasmodial effects of the treatment. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to the release of hepatic merozoites for all compounds. We also demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy does not determine antiplasmodial efficacy for these compounds.

Advances in machine-learning approaches to RNA-targeted drug design

RNA molecules play multifaceted functional and regulatory roles within cells and have garnered significant attention in recent years as promising therapeutic targets. With remarkable successes achieved by artificial intelligence (AI) in different fields such as computer vision and natural language processing, there is a growing imperative to harness AI's potential in computer-aided drug design (CADD) to discover novel drug compounds that target RNA. Although machine-learning (ML) approaches have been widely adopted in the discovery of small molecules targeting proteins, the application of ML approaches to model interactions between RNA and small molecule is still in its infancy. Compared to protein-targeted drug discovery, the major challenges in ML-based RNA-targeted drug discovery stem from the scarcity of available data resources. With the growing interest and the development of curated databases focusing on interactions between RNA and small molecule, the field anticipates a rapid growth and the opening of a new avenue for disease treatment. In this review, we aim to provide an overview of recent advancements in computationally modeling RNA-small molecule interactions within the context of RNA-targeted drug discovery, with a particular emphasis on methodologies employing ML techniques.