Current developments in antibiotic discovery: Global microbial diversity as a source for evolutionary optimized anti-bacterials: Global microbial diversity as a source for evolutionary optimized anti-bacterials

Natural products as drug leads: exploring their potential in drug discovery and development

Natural products have been pivotal in drug discovery, offering a wealth of bioactive compounds that significantly contribute to therapeutic developments. Despite the rise of synthetic chemistry, natural products continue to play a crucial role due to their unique chemical structures and diverse biological activities. This study reviews and evaluates the potential of natural products in drug discovery and development, emphasizing the integration of traditional knowledge with modern drug discovery methodologies and addressing the associated challenges. A comprehensive literature search was conducted across PubMed/MedLine, Scopus, Web of Science, Google Scholar, and Cochrane Library, covering publications from 2000 to 2023. Inclusion criteria focused on studies related to natural products, bioactive compounds, medicinal plants, phytochemistry, and AI applications in drug discovery. Data were categorized into source, extraction methods, bioactivity assays, and technological advances. The current review underscores the historical and ongoing importance of natural products in drug discovery. Technological advancements in chromatographic and spectroscopic techniques have improved the isolation and structural elucidation of bioactive compounds. AI and machine learning have streamlined the identification and optimization of natural product leads. Challenges such as biodiversity sustainability and development complexities are discussed, alongside innovative approaches like biosynthetic engineering and metagenomics. Natural products remain a vital source of novel therapeutic agents, providing unique chemical diversity and specific biological activities. Integrating traditional knowledge with modern scientific methods is essential for maximizing the potential of natural products in drug discovery. Despite existing challenges, ongoing research and technological advancements are expected to enhance the efficiency and success of natural product-based drug development.

Strategies for Actinobacteria Isolation, Cultivation, and Metabolite Production that Are Biologically Important

Novel antimicrobial agents are urgently needed to combat antimicrobial resistance from multidrug-resistant organisms. Actinobacteria are key sources of bioactive metabolites with diverse biological activities. Despite their contributions to drug discovery, the process from strain identification to drug manufacturing faces many challenges, especially the rediscovery of known compounds. Recent technological and scientific advancements have accelerated drug development. Efforts to isolate and screen rare actinobacterial species could yield novel bioactive compounds. This review summarizes techniques for selectively isolating rare actinobacteria, improving bioactive metabolite production, and discovering potential strains. Notably, new genomic strategies and new discoveries regarding spectroscopic signature-based bioactive natural products containing specific structural motifs are also discussed. Furthermore, this review updates the compounds derived from rare actinobacteria and their biological applications.

A Review on Rare and Symbiotic Actinobacteria: Emerging Biotechnological Tools Against Antimicrobial Resistance

Antimicrobial resistance (AMR) poses a global threat to public health, with projections estimating 10 million deaths annually by 2050 if current trends persist. Actinobacteria, renowned for their biosynthetic capacity, are a key source of bioactive compounds, producing over 75% of known antibiotics. The adaptability of these microorganisms allows them to thrive in diverse habitats, including extreme ones, through the production of secondary metabolites that are of paramount importance for industry. Furthermore, actinobacteria are capable of living in symbiosis with several organisms, producing metabolites to protect and promote the growth of the host in exchange for nutrients and shelter. Some of these metabolites, such as antibiotics, play a key role in combating host pathogens and can be biotechnologically exploited to combat human resistant pathogens. This review presents the origins of AMR, the unique biology of actinobacteria, as well as their diverse biosynthetic pathways and their role in mitigating the AMR crisis. It also highlights the need for innovative biotechnological strategies for the isolation of rare and understudied actinobacteria, as symbiotic actinobacteria, to avoid rediscovery of molecules while finding new potential natural products and scaffolds for synthetic drugs. By providing a better understanding of their ecological, genomic, and metabolic diversity, this review provides valuable insights into the exploration of rare and symbiotic actinobacteria for developing antimicrobial solutions.

Nanoceria Anti-inflammatory and Antimicrobial Nanodrug: Cellular and Molecular Mechanism of Action

INTRODUCTION

Nanoceria is a well-known nanomaterial with various properties, including antioxidant, proangiogenic, and therapeutic effects. Despite its potential, there are still aspects that require further exploration, particularly its anti-inflammatory and antimicrobial activities.

METHODS

The global demand for novel anti-inflammatory and antimicrobial drugs underscores the significance of understanding nanoceria in both contexts. In this study, we evaluated the effect of nanoceria on macrophage polarization to better understand its anti-inflammatory effects. Additionally, we investigated the mechanism of action of nanoceria against Cryptococcus neoformans (ATCC 32045), Candida parapsilosis (ATCC 22019), Candida krusei (ATCC 6258), and Candida albicans.

RESULTS

The results demonstrated that nanoceria can polarize macrophages toward an anti-inflammatory profile, revealing the cellular mechanisms involved in the anti-inflammatory response. Concerning the antimicrobial effect, it was observed that nanoceria have a more pronounced impact on Candida parapsilosis, leading to the formation of pronounced pores on the surface of this species.

CONCLUSION

Finally, biochemical analysis revealed transitory alterations, mainly in liver enzymes. The data support the use of nanoceria as a potential anti-inflammatory and antimicrobial drug and elucidate some of the mechanisms involved, shedding light on the properties of this nanodrug.

Compounds Containing 2,3-Bis(phenylamino) Quinoxaline Exhibit Activity Against Methicillin-Resistant Staphylococcus aureus, Enterococcus faecalis, and Their Biofilms

Antimicrobial resistance remains a global issue, hindering the control of bacterial infections. This study examined the antimicrobial properties of 2,3-N,N-diphenyl quinoxaline derivatives against Gram-positive, Gram-negative, and Mycobacterium species. Two quinoxaline derivatives (compounds 25 and 31) exhibited significant activity against most strains of Staphylococcus aureus, Enterococcus faecium, and Enterococcus faecalis tested, with MIC values ranging from 0.25 to 1 mg/L. These compounds also showed effective antibacterial activity against methicillin-resistant S. aureus (MRSA) and vancomycin-resistant E. faecium/E. faecalis (VRE) strains. They demonstrated comparable or superior activity to four current antibiotics (vancomycin, teicoplanin, daptomycin, and linezolid) against a wide range of clinically relevant isolates. Additionally, they were more effective in preventing S. aureus and E. faecalis biofilm formation compared to several other antibiotics. In summary, these two quinoxaline derivatives have potential as new antibacterial agents.

Bioluminescent Whole-Cell Bioreporter Bacterial Panel for Sustainable Screening and Discovery of Bioactive Compounds Derived from Mushrooms

This study presents a rapid and comprehensive method for screening mushroom extracts for the putative discovery of bioactive molecules, including those exhibiting antimicrobial activity. This approach utilizes a panel of bioluminescent bacteria, whose light production is a sensitive indicator of various cellular effects triggered by the extracts, including disruption of bacterial communication (quorum sensing), protein and DNA damage, fatty acid metabolism alterations, and oxidative stress induction. The bioassay's strength is its ability to efficiently analyze a large number of extracts simultaneously while also assessing several different mechanisms of toxicity, significantly reducing screening time. All samples analyzed exhibited more than one cellular effect, as indicated by the reporter bacteria. Four samples (C. cornucopioides, F. fomentarius, I. obliquus, and M. giganteus) displayed the highest number (six) of possible mechanisms of antibacterial activity. Additionally, combining extraction and purification protocols with a bioluminescent bacterial panel enables simultaneous improvement of the desired antimicrobial properties of the extracts. The presented approach offers a valuable tool for uncovering the diverse antimicrobial mechanisms of mushroom extracts.

Advances in methods and concepts provide new insight into antibiotic fluxes across the bacterial membrane

The sophisticated envelope of Gram-negative bacteria modulates the uptake of small molecules in a side-chain-sensitive manner. Despite intensive theoretical and experimental investigations, a general set of pathways underpinning antibiotic uptake has not been identified. This manuscript discusses the passive influx versus active efflux of antibiotics, considering the responsible membrane proteins and the transported molecules. Recent methods have analyzed drug transport across the bacterial membrane in order to understand their activity. The combination of in vitro, in cellulo and in silico methods shed light on the key, mainly electrostatic, interactions between the molecule surface, porins and transporters during permeation. A key factor is the relationship between the dose of an active compound near its target and its antibacterial activity during the critical early window. Today, methodology breakthroughs provide fruitful tools to precisely dissect drug transport, identify key steps in drug resistance associated with membrane impermeability and efflux, and highlight key parameters to generate more effective drugs.

A systematic approach to determine the outcome of the competition between two microbial species in bioreactor cocultures

The two-species microbial cocultures are effective in terms of awakening the cryptic biosynthetic pathways. They may also lead to the improved production of previously discovered molecules. Importantly, only a few outcomes of the cocultures may prove desirable, namely those leading to the formation of useful secondary metabolites. To address this issue, a method allowing for the evaluation of the final outcome of the co-culture process and fine-tune the cocultivation strategy was proposed. The systematic approach was supported by the experimental data from the bioreactor runs with the participation of Aspergillus terreus and Penicillium rubens confronted with Streptomyces rimosus and Streptomyces noursei. Kinetic, morphological and metabolic aspects of dominance were analysed via the newly proposed formula describing the dominance pattern. The suggested method involved the determination of the numerical value representing the dominance level. When it was high (value 1) no useful metabolites were formed apart from those originating from the winning counterpart. But either for the partial dominances or when the winning organism changed within the run or when the competition ended in draw, the number of the secondary metabolites of interest in the broth was the highest. Next, the systematic approach illustrated how the delayed inoculation strategy influenced the level of dominance leading to the change of winning counterpart and the set of metabolites produced. The proposed systematic approach allows for the reliable determination of the level of dominance in the two-species cocultures to seek for the potentially useful substances for future applications.

Harnessing Gram-negative bacteria for novel anti-Gram-negative antibiotics

Natural products have proven themselves as a valuable resource for antibiotics. However, in view of increasing antimicrobial resistance, there is an urgent need for new, structurally diverse agents that have the potential to overcome resistance and treat Gram-negative pathogens in particular. Historically, the search for new antibiotics was strongly focussed on the very successful Actinobacteria. On the other hand, other producer strains have been under-sampled and their potential for the production of bioactive natural products has been underestimated. In this mini-review, we highlight prominent examples of novel anti-Gram negative natural products produced by Gram-negative bacteria that are currently in lead optimisation or preclinical development. Furthermore, we will provide insights into the considerations and strategies behind the discovery of these agents and their putative applications.

Ultrasound-Mediated Antibiotic Delivery to In Vivo Biofilm Infections: A Review

Bacterial biofilms are a significant concern in various medical contexts due to their resilience to our immune system as well as antibiotic therapy. Biofilms often require surgical removal and frequently lead to recurrent or chronic infections. Therefore, there is an urgent need for improved strategies to treat biofilm infections. Ultrasound-mediated drug delivery is a technique that combines ultrasound application, often with the administration of acoustically-active agents, to enhance drug delivery to specific target tissues or cells within the body. This method involves using ultrasound waves to assist in the transportation or activation of medications, improving their penetration, distribution, and efficacy at the desired site. The advantages of ultrasound-mediated drug delivery include targeted and localized delivery, reduced systemic side effects, and improved efficacy of the drug at lower doses. This review scrutinizes recent advances in the application of ultrasound-mediated drug delivery for treating biofilm infections, focusing on in vivo studies. We examine the strengths and limitations of this technology in the context of wound infections, device-associated infections, lung infections and abscesses, and discuss current gaps in knowledge and clinical translation considerations.

Development of Fragment-Based Inhibitors of the Bacterial Deacetylase LpxC with Low Nanomolar Activity

In a fragment-based approach using NMR spectroscopy, benzyloxyacetohydroxamic acid-derived inhibitors of the bacterial deacetylase LpxC bearing a substituent to target the uridine diphosphate-binding site of the enzyme were developed. By appending privileged fragments via a suitable linker, potent LpxC inhibitors with promising antibacterial activities could be obtained, like the one-digit nanomolar LpxC inhibitor (S)-13j [Ki (EcLpxC C63A) = 9.5 nM; Ki (PaLpxC): 5.6 nM]. To rationalize the observed structure-activity relationships, molecular docking and molecular dynamics studies were performed. Initial in vitro absorption-distribution-metabolism-excretion-toxicity (ADMET) studies of the most potent compounds have paved the way for multiparameter optimization of our newly developed isoserine-based amides.

Retention of methicillin susceptibility in Staphylococcus aureus using natural adjuvant as an allosteric modifier of penicillin-binding protein 2a

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant global public health challenge due to its resistance to conventional antibiotics, primarily mediated by the mutated penicillin-binding protein, PBP2a. This study aims to investigate the potential of phytochemicals derived from medicinal plants in the Indian subcontinent to serve as adjuvants, enhancing the efficacy of methicillin against MRSA through allosteric modification of PBP2a using molecular docking and molecular dynamics (MD) simulation. After comprehensive Absorption, Distribution, Metabolism, and Excretion (ADME) profiling, along with AMES and hepatotoxicity tests, 9 compounds were shortlisted as suitable adjuvant candidates. Among them, nimbolide, quercetin, emodin, daidzein, eriodictyol, luteolin, and apigenin exhibited strong binding affinity to the allosteric site of PBP2a, with docking scores ranging from -8.7 to -7.3 kcal/mol. These phytochemicals facilitated enhanced methicillin binding, as evidenced by improved docking scores ranging from -6.1 to -6.8 kcal/mol, compared to -5.6 kcal/mol for methicillin alone. Molecular dynamics simulations confirmed the stability and favorable conformations of phytochemical-PBP2a complexes. Quercetin and daidzein were identified as the most promising adjuvant candidates, forming stable and energetically favorable complexes with PBP2a. Experimental validation showed that quercetin, at 30 mg/mL, effectively retained methicillin's antibacterial efficacy against MRSA. This study underscores the potential of natural compounds in overcoming antibiotic resistance and suggests that phytochemical-antibiotic synergism could be a viable strategy to combat multidrug-resistant bacterial infections.

Combating bacterial biofilms and related drug resistance: Role of phyto-derived adjuvant and nanomaterials

The emergence of antimicrobial resistance (AMR) in clinical microbes has led to a search for novel antibiotics for combating bacterial infections. The treatment of bacterial infections becomes more challenging with the onset of biofilm formation. AMR is further accelerated by biofilm physiology and differential gene expression in bacteria with an inherent resistance to conventional antibiotics. In the search for innovative strategies to control the spread of AMR in clinical isolates, plant-derived therapeutic metabolites can be repurposed to control biofilm-associated drug resistance. Unlike antibiotics, designed to act on a single cellular process, phytochemicals can simultaneously target multiple cellular components. Furthermore, they can disrupt biofilm formation and inhibit quorum sensing, offering a comprehensive approach to combat bacterial infections. In bacterial biofilms, the first line of AMR is due to biofilms associated with the extracellular matrix, diffusion barriers, quorum sensing, and persister cells. These extracellular barriers can be overcome using phytochemical-based antibiotic adjuvants to increase the efficacy of antibiotic treatment and restrict the spread of AMR. Furthermore, phytochemicals can be used to target bacterial intracellular machinery such as DNA replication, protein synthesis, efflux pumps, and degrading enzymes. In parallel with pristine phytochemicals, phyto-derived nanomaterials have emerged as an effective means of fighting bacterial biofilms. These nanomaterials can be formulated to cross the biofilm barriers and function on cellular targets. This review focuses on the synergistic effects of phytochemicals and phyto-derived nanomaterials in controlling the progression of biofilm-related AMR. IT provides comprehensive insights into recent advancements and the underlying mechanisms of the use of phyto-derived adjuvants and nanomaterials.

Triazole-Bridged Peptides with Enhanced Antimicrobial Activity and Potency against Pathogenic Bacteria

There are still no linear antimicrobial peptides (AMPs) available as a treatment option against bacterial infections. This is caused by several drawbacks that come with AMPs such as limited proteolytic stability and low selectivity against human cells. In this work, we screened a small library of rationally designed new peptides based on the cell-penetrating peptide sC18* toward their antimicrobial activity. We identified several effective novel AMPs and chose one out of this group to further increase its potency. Therefore, we introduced a triazole bridge at different positions to provide a preformed helical structure, assuming that this modification would improve (i) proteolytic stability and (ii) membrane activity. Indeed, placing the triazole bridge within the hydrophilic part of the linear analogue highly increased membrane activity as well as stability against enzymatic digestion. The new peptides, 8A and 8B, demonstrated high activity against several bacterial species tested including pathogenic N. gonorrhoeae and methicillin-resistant S. aureus. Since they exhibited significantly good tolerability against human fibroblast and blood cells, these novel peptides offer true alternatives for future clinical applications and are worth studying in more detail.

Secondary metabolite profile of Streptomyces spp. changes when grown with the sub-lethal concentration of silver nanoparticles: possible implication in novel compound discovery

The decline of new antibiotics and the emergence of multidrug resistance in pathogens necessitates a revisit of strategies used for lead compound discovery. This study proposes to induce the production of bioactive compounds with sub-lethal concentrations of silver nanoparticles (Ag-NPs). A total of Forty-two Actinobacteria isolates from four Saudi soil samples were grown with and without sub-lethal concentration of Ag-NPs (50 µg ml-1). The spent broth grown with Ag-NPs, or without Ag-NPs were screened for antimicrobial activity against four bacteria. Interestingly, out of 42 strains, broths of three strains grown with sub-lethal concentration of Ag-NPs exhibit antimicrobial activity against Staphylococcus aureus and Micrococcus luteus. Among these, two strains S4-4 and S4-21 identified as Streptomyces labedae and Streptomyces tirandamycinicus based on 16S rRNA gene sequence were selected for detailed study. The change in the secondary metabolites profile in the presence of Ag-NPs was evaluated using GC-MS and LC-MS analyses. Butanol extracts of spent broth grown with Ag-NPs exhibit strong antimicrobial activity against M. luteus and S. aureus. While the extracts of the controls with the same concentration of Ag-NPs do not show any activity. GC-analysis revealed a clear change in the secondary metabolite profile when grown with Ag-NPs. Similarly, the LC-MS patterns also differ significantly. Results of this study, strongly suggest that sub-lethal concentrations of Ag-NPs influence the production of secondary metabolites by Streptomyces. Besides, LC-MS results identified possible secondary metabolites, associated with oxidative stress and antimicrobial activities. This strategy can be used to possibly induce cryptic biosynthetic gene clusters for the discovery of new lead compounds.

Discovery of a lagriamide polyketide by integrated genome mining, isotopic labeling, and untargeted metabolomics

Microorganisms from the order Burkholderiales have been the source of a number of important classes of natural products in recent years. For example, study of the beetle-associated symbiont Burkholderia gladioli led to the discovery of the antifungal polyketide lagriamide; an important molecule from the perspectives of both biotechnology and chemical ecology. As part of a wider project to sequence Burkholderiales genomes from our in-house Burkholderiales library we identified a strain containing a biosynthetic gene cluster (BGC) similar to the original lagriamide BGC. Structure prediction failed to identify any candidate masses for the products of this BGC from untargeted metabolomics mass spectrometry data. However, genome mining from publicly available databases identified fragments of this BGC from a culture collection strain of Paraburkholderia. Whole genome sequencing of this strain revealed the presence of a homologue of this BGC with very high sequence identity. Stable isotope feeding of the two strains in parallel using our newly developed IsoAnalyst platform identified the product of this lagriamide-like BGC directly from the crude fermentation extracts, affording a culturable supply of this interesting compound class. Using a combination of bioinformatic, computational and spectroscopic methods we defined the absolute configurations for all 11 chiral centers in this new metabolite, which we named lagriamide B. Biological testing of lagriamide B against a panel of 21 bacterial and fungal pathogens revealed antifungal activity against the opportunistic human pathogen Aspergillus niger, while image-based Cell Painting analysis indicated that lagriamide B also causes actin filament disruption in U2-OS osteosarcoma cells.

Going to extremes: progress in exploring new environments for novel antibiotics

The discoveries of penicillin and streptomycin were pivotal for infection control with the knowledge subsequently being used to enable the discovery of many other antibiotics currently used in clinical practice. These valuable compounds are generally derived from mesophilic soil microorganisms, predominantly Streptomyces species. Unfortunately, problems with the replication of results suggested that this discovery strategy was no longer viable, motivating a switch to combinatorial chemistry in conjunction with existing screening programmes to derive new antimicrobials. However, the chemical space occupied by these synthetic products is vastly reduced compared to those of natural products. More recent approaches such as using artificial intelligence to 'design' synthetic ligands to dock with molecular targets suggest that chemical synthesis is still a promising option for discovery. It is important to employ diverse discovery strategies to combat the worrying increase in antimicrobial resistance (AMR). Here, we reconsider whether nature can supply innovative solutions to recalcitrant infections. Specifically, we assess progress in identifying novel antibiotic-producing organisms from extreme and unusual environments. Many of these organisms have adapted physiologies which often means they produce different repertoires of bioactive metabolites compared to their mesophilic counterparts, including antibiotics. In addition, we examine insights into the regulation of extremotolerant bacterial physiologies that can be harnessed to increase the production of clinically important antibiotics and stimulate the synthesis of new antibiotics in mesophilic microorganisms. Finally, we comment on the insights provided by combinatorial approaches to the treatment of infectious diseases that might enhance the efficacy of antibiotics and reduce the development of AMR.

The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide

Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.

LL-37: Structures, Antimicrobial Activity, and Influence on Amyloid-Related Diseases

Antimicrobial peptides (AMPs), as well as host defense peptides (HDPs), constitute the first line of defense as part of the innate immune system. Humans are known to express antimicrobial precursor proteins, which are further processed to generate AMPs, including several types of α/β defensins, histatins, and cathelicidin-derived AMPs like LL37. The broad-spectrum activity of AMPs is crucial to defend against infections caused by pathogenic bacteria, viruses, fungi, and parasites. The emergence of multi-drug resistant pathogenic bacteria is of global concern for public health. The prospects of targeting antibiotic-resistant strains of bacteria with AMPs are of high significance for developing new generations of antimicrobial agents. The 37-residue long LL37, the only cathelicidin family of AMP in humans, has been the major focus for the past few decades of research. The host defense activity of LL37 is likely underscored by its expression throughout the body, spanning from the epithelial cells of various organs-testis, skin, respiratory tract, and gastrointestinal tract-to immune cells. Remarkably, apart from canonical direct killing of pathogenic organisms, LL37 exerts several other host defense activities, including inflammatory response modulation, chemo-attraction, and wound healing and closure at the infected sites. In addition, LL37 and its derived peptides are bestowed with anti-cancer and anti-amyloidogenic properties. In this review article, we aim to develop integrative, mechanistic insight into LL37 and its derived peptides, based on the known biophysical, structural, and functional studies in recent years. We believe that this review will pave the way for future research on the structures, biochemical and biophysical properties, and design of novel LL37-based molecules.

Biofilm-Inhibitory Activity of Wild Mushroom Extracts against Pathogenic Bacteria

Objective

This study aims to investigate the bacterial biofilm-inhibitory effect of mushroom extracts.

Methods

Mushrooms were collected from Arabuko-Sokoke and Kakamega forests and identified using morphological and molecular approaches. Auricularia auricula-judae, Microporus xanthopus, Termitomyces umkowaani, Trametes elegans, and Trametes versicolor were extracted by chloroform, 70% ethanol, and hot water. Extracts were tested against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus (ATCC25923). Data were analyzed using SPSS ver. 20.0.

Results

Chloroform, 70% ethanol, and hot water extracts of A. auricula-judae (50 μg/mL) showed statistically significant antibiofilm activities against P. aeruginosa, E. coli, and S. aureus (p ≤ 0.05). M. xanthopus extracts (250 μg/mL) revealed significantly significant antibiofilm activities against each test bacterium (p ≤ 0.05). All extracts of T. umkowaani (250 μg/mL) exhibited statistically significant antibiofilm activities against S. aureus only (p ≤ 0.05). Chloroform extract of T. elegans (250 μg/mL) showed the best antibiofilm activity (69.75 ± 0.01%) against S. aureus. All T. versicolor extracts (250 μg/mL) indicated the best antibiofilm activities against S. aureus.

Conclusions

Being the first study of its kind to be conducted in Kenya, it added a novel concept to the body of knowledge already known about medical biotechnology research. It offers a fresh understanding of the various varieties of mushrooms found in Kenya, their potential biological function in the production of drugs, particularly those that combat drug resistance, and perhaps even a peek at their bioactive elements. Wild mushrooms, a hidden gem, might help to reopen the pipeline of new antibiotics that have been on the decline. However, further research is required to determine the potential mechanism(s) of action of the extracts that are in charge of the apparent antibiofilm activity.

Investigating the Stirred Tank Bioreactor Co-Cultures of the Secondary Metabolite Producers Streptomyces noursei and Penicillium rubens

The stirred tank bioreactor co-cultures of the filamentous fungus Penicillium rubens and actinomycete Streptomyces noursei were studied with regard to secondary metabolite (SM) production, sugar consumption, and dissolved oxygen levels. In addition to the quantitative analysis of penicillin G and nystatin A1, the broad repertoire of 22 putatively identified products was semi-quantitatively evaluated with the use of UPLC-MS. Three co-cultivation variants differing with respect to the co-culture initiation method (i.e., the simultaneous inoculation of P. rubens and S. noursei and the 24 or 48 h inoculation delay of S. noursei relative to P. rubens) were investigated. All the co-cultures were carried out in parallel with the corresponding monoculture controls. Even though S. noursei showed the tendency to outperform P. rubens and inhibit the production of fungal secondary metabolites, the approach of simultaneous inoculation was effective in terms of enhancing the production of some S. noursei SMs, namely desferrioxamine E, deshydroxynocardamine, and argvalin. S. noursei displayed the capability of adaptation and SM production even after being inoculated into the 24 or 48 h culture of P. rubens. Interestingly, S. noursei turned out to be more efficient in terms of secondary metabolite production when its inoculation time relative to P. rubens was delayed by 48 h rather than by 24 h. The study demonstrated that the prolongation of inoculation delays can be beneficial for production-related performance in some co-culture systems.

Evaluation of Gold Complexes to Address Bacterial Resistance, Quorum Sensing, Biofilm Formation, and Their Antiviral Properties against Bacteriophages

The worldwide increase in antibiotic resistance poses a significant challenge, and researchers are diligently seeking new drugs to combat infections and prevent bacterial pathogens from developing resistance. Gold (I and III) complexes are suitable for this purpose. In this study, we tested four gold (I and III) complexes, (1) chlorotrimethylphosphine gold(I); (2) chlorotriphenylphosphine gold(I); (3) dichloro(2-pyridinecarboxylate) gold (III); and (4) 1,3-bis(2,6-diisopropylphenyl)imidazole-2-ylidene gold(I) chloride, for their antibacterial, antibiofilm, antiviral, and anti-quorum sensing activities. Results reveal that 1 significantly inhibits Escherichia coli DSM 1077 and Staphylococcus aureus ATCC 6538, while 2, 3, and 4 only inhibit S. aureus ATCC 6538. The minimum inhibitory concentration (MIC) of 1 for S. aureus ATCC 6538 is 0.59 μg/mL (1.91 μM), and for methicillin-resistant S. aureus strains MRSA 12 and MRSA 15, it is 1.16 μg/mL (3.75 μM). For E. coli DSM 1077 (Gram-negative), the MIC is 4.63 μg/mL (15 μM), and for multi-resistant E. coli I731940778-1, it is 9.25 μg/mL (30 μM). Complex 1 also disrupts biofilm formation in E. coli and S. aureus after 6 h or 24 h exposure. Moreover, 1 and 2 inhibit the replication of two enterobacteria phages. Anti-quorum sensing potential still requires further clarification. These findings highlight the potential of gold complexes as effective agents to combat bacterial and viral infections.

Identification of the lipodepsipeptide selethramide encoded in a giant nonribosomal peptide synthetase from a Burkholderia bacterium

Bacterial natural products have found many important industrial applications. Yet traditional discovery pipelines often prioritize individual natural product families despite the presence of multiple natural product biosynthetic gene clusters in each bacterial genome. Systematic characterization of talented strains is a means to expand the known natural product space. Here, we report genomics, epigenomics, and metabolomics studies of Burkholderia sp. FERM BP-3421, a soil isolate and known producer of antitumor spliceostatins. Its genome is composed of two chromosomes and two plasmids encoding at least 29 natural product families. Metabolomics studies showed that FERM BP-3421 also produces antifungal aminopyrrolnitrin and approved anticancer romidepsin. From the orphan metabolome features, we connected a lipopeptide of 1,928 Da to an 18-module nonribosomal peptide synthetase encoded as a single gene in chromosome 1. Isolation and structure elucidation led to the identification of selethramide which contains a repeating pattern of serine and leucine and is cyclized at the side chain oxygen of the one threonine residue at position 13. A (R)-3-hydroxybutyric acid moiety decorates the N-terminal serine. Initial attempts to obtain deletion mutants to probe the role of selethramide failed. After acquiring epigenome (methylome) data for FERM BP-3421, we employed a mimicry by methylation strategy that improved DNA transfer efficiency. Mutants defective in selethramide biosynthesis showed reduced surfactant activity and impaired swarming motility that could be chemically complemented with selethramide. This work unveils a lipopeptide that promotes surface motility, establishes improved DNA transfer efficiency, and sets the stage for continued natural product identification from a prolific strain.

Codeine dysregulates ribosome biogenesis in Escherichia coli with DNA double-strand breaks to chart path to new classes of antibiotics

Aim

A bacterial genetics-guided approach was utilized for the discovery of new compounds affecting bacterial genome stability.

Materials & methods

Fungal extracts and fractions were tested for genome instability-mediated antibacterial activity. Interaction assays and RT-qPCR were used to identify compounds that boost the activity of sub-minimum inhibitory concentration streptomycin and obtain insights on the molecular mechanisms of the primary hit compound, respectively.

Results

Several extracts and fractions caused bacterial genome instability. Codeine, in synergy with streptomycin, regulates double-strand break (DSB) repair and causes bacterial ribosome dysfunction in the absence of DSBs, and dysregulation of ribosome biogenesis in a DSB-dependent manner.

Conclusion

This study demonstrates a potential viable strategy that we are exploring for the discovery of new chemical entities with activities against Escherichia coli and other bacterial pathogens.

Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview

Co-cultivation is an effective method of inducing the production of specialized metabolites (SMs) in microbial strains. By mimicking the ecological interactions that take place in natural environment, this approach enables to trigger the biosynthesis of molecules which are not formed under monoculture conditions. Importantly, microbial co-cultivation may lead to the discovery of novel chemical entities of pharmaceutical interest. The experimental efforts aimed at the induction of SMs are greatly facilitated by computational techniques. The aim of this overview is to highlight the relevance of computational methods for the investigation of SM induction via microbial co-cultivation. The concepts related to the induction of SMs in microbial co-cultures are briefly introduced by addressing four areas associated with the SM induction workflows, namely the detection of SMs formed exclusively under co-culture conditions, the annotation of induced SMs, the identification of SM producer strains, and the optimization of fermentation conditions. The computational infrastructure associated with these areas, including the tools of multivariate data analysis, molecular networking, genome mining and mathematical optimization, is discussed in relation to the experimental results described in recent literature. The perspective on the future developments in the field, mainly in relation to the microbiome-related research, is also provided.

An Update Review of Approaches to Multiple Action-Based Antibacterials

Many approaches are being pursued to address the major global health challenge posed by the increasing resistance of pathogenic bacteria to antibacterial agents. One of the promising approaches being investigated includes the design and development of multiple action-based small-molecule antibacterials. Aspects of this broad area have been reviewed previously, and recent developments are addressed in this update review covering the literature mainly over the past three years. Considerations encompassing drug combinations, single-molecule hybrids and prodrugs are summarised in regard to the intentional design and development of multiple-action agents with a focus on potential triple or greater activities in bacteria. The hope for such single agents or combinations of single agents is that resistance development will be significantly hindered, and they may be useful in tackling bacterial disease caused by both resistant and non-resistant bacteria.

Bacterial natural product discovery by heterologous expression

Natural products have found important applications in the pharmaceutical and agricultural sectors. In bacteria, the genes that encode the biosynthesis of natural products are often colocalized in the genome, forming biosynthetic gene clusters. It has been predicted that only 3% of natural products encoded in bacterial genomes have been discovered thus far, in part because gene clusters may be poorly expressed under laboratory conditions. Heterologous expression can help convert bioinformatics predictions into products. However, challenges remain, such as gene cluster prioritization, cloning of the complete gene cluster, high level expression, product identification, and isolation of products in practical yields. Here we reviewed the literature from the past 5 years (January 2018 to June 2023) to identify studies that discovered natural products by heterologous expression. From the 50 studies identified, we present analyses of the rationale for gene cluster prioritization, cloning methods, biosynthetic class, source taxa, and host choice. Combined, the 50 studies led to the discovery of 63 new families of natural products, supporting heterologous expression as a promising way to access novel chemistry. However, the success rate of natural product detection varied from 11% to 32% based on four large-scale studies that were part of the reviewed literature. The low success rate makes it apparent that much remains to be improved. The potential reasons for failure and points to be considered to improve the chances of success are discussed.

ONE-SENTENCE SUMMARY

At least 63 new families of bacterial natural products were discovered using heterologous expression in the last 5 years, supporting heterologous expression as a promising way to access novel chemistry; however, the success rate is low (11-32%) making it apparent that much remains to be improved-we discuss the potential reasons for failure and points to be considered to improve the chances of success. BioRender was used to generate the graphical abstract figure.