Antibiotic drug discovery: Challenges and perspectives in the light of emerging antibiotic resistance

Identifying Opportunity Targets in Gram-Negative Pathogens for Infectious Disease Mitigation

Antimicrobial drug resistance (AMR) is a pressing global human health challenge. Humans face one of their grandest challenges as climate change expands the habitat of vectors that bear human pathogens, incidences of nosocomial infections rise, and new antibiotics discovery lags. AMR is a multifaceted problem that requires a multidisciplinary and an "all-hands-on-deck" approach. As chemical microbiologists, we are well positioned to understand the complexities of AMR while seeing opportunities for tackling the challenge. In this Outlook, we focus on vulnerabilities of human pathogens and posit that they represent "opportunity targets" for which few modulatory ligands exist. We center our attention on proteins in Gram-negative organisms, which are recalcitrant to many antibiotics because of their external membrane barrier. Our hope is to highlight such targets and explore their potential as "druggable" proteins for infectious disease mitigation. We posit that success in this endeavor will introduce new classes of antibiotics that might alleviate some of the current pressing AMR concerns.

Antimicrobial lipids loaded on lectin display reduced MIC, curtail pathogenesis and protect zebrafish from reinfection by immunomodulation

Antibiotic resistance and re-emergence of highly resistant pathogens is a grave concern everywhere and this has consequences for all kinds of human activities. Herein, we showed that N-palmitoylethanolamine-derived cationic lipid (cN16E) had a lower minimum inhibitory concentration (MIC) against both Gram-positive and Gram-negative bacteria when it was loaded with Butea monosperma seed lectin (BMSL). The analysis using lectin-FITC conjugate labelling indicated that the improved antibacterial activity of BMSL conjugation was due to bacterial cell surface glycan recognition. Live and dead staining experiments revealed that the BMSL-cN16E conjugate (BcN16E) exerts antibacterial activity by damaging the bacterial membrane. BcN16E antimicrobial activity was demonstrated using an infected zebrafish animal model because humans have 70 % genetic similarity to zebrafish. BcN16E therapeutic potential was established successfully by rescuing fish infected with uropathogenic Escherichia coli (UPEC). Remarkably, the rescued infected fish treated with BcN16E prevented reinfection without further therapy, indicating BcN16E immunomodulatory potential. Thus, the study examined the expression of immune-related genes, including tnfα, ifnγ, il-1β, il-4, il-10, tlr-2, etc. There was a significant elevation in the expression of all these genes compared to control and fish treated with BMSL or cN16E alone. Interestingly, when the rescued zebrafish were reinfected with the same pathogen, the levels of expression of these genes were many folds higher than seen earlier. Radial immune diffusion analyses (RIA) using zebrafish serum revealed antibody production during the initial infection and treatment. Interestingly, reinfected fish had significant immunoprecipitation in RIA, a feature absent in the groups treated with cN16E, BMSL, and control. These results clearly show that the BcN16E complex not only rescued infected zebrafish but also conferred long-lasting protection in terms of immunomodulation that protects against multiple reinfections. The findings support that BcN16E has immense potential as a novel immunostimulant for various biomedical applications.

Prevalence, pandemic, preventions and policies to overcome antimicrobial resistance

Antimicrobial resistance (AMR) is a growing concern in Asia, and it is essential to understand the prevalence, pandemic, prevention, and policies to overcome it. According to the World Health Organization (WHO), AMR is one of the main causes of death; in 2019, it was linked to 4.95 million fatalities and caused about 1.27 million deaths. A core package of actions has been provided by WHO to help countries prioritize their needs when creating, carrying out, and overseeing national action plans on antimicrobial resistance. Using a people-cantered approach to AMR, the interventions address the needs and obstacles that individuals and patients encounter when trying to obtain healthcare. The people-cantered core package of AMR treatments seeks to improve public and policymakers; awareness and comprehension of AMR by changing the narrative of AMR to emphasize the needs of people and systemic impairments. Additionally, it backs a more comprehensive and programmatic national response to AMR, which emphasizes the value of fair and inexpensive access to high-quality healthcare services for the avoidance, identification, and management of drug-resistant diseases. The report signals increasing resistance to antibiotics in bacterial infections in humans and the need for better data. In conclusion, the prevalence of AMR in Asia is a significant public health concern, and it is crucial to implement policies and interventions to overcome it.

Diversity, molecular phylogenetics, and antibiotic biosynthetic potential of endophytic Actinobacteria isolated from medicinal plants in Nigeria

Actinobacteria that are found in nature have enormous promise for the growth of the pharmaceutical sector. There is a scarce report on the antimicrobial activities of endophytic Actinobacteria from Nigeria. As a result, this study evaluated the Actinobacteria isolated from Nigerian medicinal plants in terms of their biodiversity, phylogenetics, and ability to produce antimicrobial compounds. Following accepted practices, Actinobacteria were isolated from the surface-sterilized plant parts. They were identified using 16S rRNA sequencing, microscopic, and morphological methods. The cell-free broth of Actinobacteria isolates was subjected to antimicrobial assay by agar well diffusion. Molecular evolutionary and genetic analysis (MEGA) version X was used for phylogenetic analysis, and the interactive tree of life (iTOL) version 6.0 was used to view the neighbour-joining method-drawn tree. A total of 13 Actinobacteria were recovered, belonging to three genera including 10 strains of Streptomyces, 2 strains of Saccharomonospora, and only 1 strain of Saccharopolyspora. They showed inhibitory activity against several bacterial pathogens. The phylogenetic tree generated from the sequences showed that our isolates are divergent and distinct from other closely related strains on the database. Further, optimization of the antibiotic production by selected Saccharomonospora sp. PNSac2 was conducted. It showed that the optimal conditions were the ISP2 medium (1-2% w/v salt) adjusted to pH of 8 at 30-32℃ for 12-14 days. In conclusion, endophytic Actinobacteria dwelling in Nigerian soils could be a promising source of new antibiotics. Future research is warranted because more genomic analysis and characterization of their metabolites could lead to the development of new antibacterial medicines.

Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing

Antibiotic effectiveness depends on a variety of factors. While many mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. A common observation is that death rate in antibiotics rises linearly with growth rate; however, it remains unclear how other factors, such as environmental conditions and whole-cell physiological properties, affect bactericidal activity. To address this, we developed a high-throughput assay to precisely measure antibiotic-mediated death. We found that death rate is linear in growth rate, but the slope depends on environmental conditions. Growth under stress lowers death rate compared to nonstressed environments with similar growth rate. To understand stress's role, we developed a mathematical model of bacterial death based on resource allocation that includes a stress-response sector; we identify this sector using RNA-seq. Our model accurately predicts the minimal inhibitory concentration (MIC) with zero free parameters across a wide range of growth conditions. The model also quantitatively predicts death and MIC when sectors are experimentally modulated using cyclic adenosine monophosphate (cAMP), including protection from death at very low cAMP levels. The present study shows that different conditions with equal growth rate can have different death rates and establishes a quantitative relation between growth, death, and MIC that suggests approaches to improve antibiotic efficacy.

Neighbours in nodules: the interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes of alder

In the present study, we report the in vitro interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes (NFNE) isolated from alder. The supernatant of NFNE grown in nitrogen-replete medium had neutral or negative effects on Frankia growth; none had a stimulatory effect. Inhibitory effects were observed for supernatants of some NFNE, notably Micromonospora, Pseudomonas, Serratia and Stenotrophomonas isolates. However, some NFNE-Frankia coculture supernatants could stimulate Frankia growth when used as a culture medium supplement. This was observed for supernatants of Frankia cocultured with Microvirga and Streptomyces isolates. In nitrogen-limited conditions, cocultures of Frankia with some NFNE, including some rhizobia and Cytobacillus, resulted in higher total biomass than Frankia-only cultures, suggesting cooperation, while other NFNE were strongly antagonistic. Microscopic observation of cocultures also revealed compromised Frankia membrane integrity, and some differentiation into stress resistance-associated morphotypes such as sporangia and reproductive torulose hyphae (RTH). Furthermore, the coculture of Frankia with Serratia sp. isolates resulted in higher concentrations of the auxinic plant hormone indole-3-acetic acid and related indolic compounds in the culture supernatant. This study sheds new light on the breadth of microbial interactions that occur amongst bacteria that inhabit the understudied ecological niche of the alder nodule.

Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment

A polyphasic approach was used to determine the taxonomic position of a marine actinomycete, designated isolate CWH03T, which we previously reported to produce new linear azole-containing peptides spongiicolazolicins A and B. Strain CWH03T is mesophilic, neutrophilic, and halotolerant streptomycete that forms spiral spore chains on aerial mycelium. Comparative 16S rRNA gene sequencing showed that CWH03T was most closely related to Streptomyces tirandamycinicus HNM0039T (99.7%), Streptomyces spongiicola HNM0071T (99.4%), 'Streptomyces marianii' ICN19T (99.1%) and Streptomyces wuyuanensis CGMCC4.7042T (99.0%). The phylogenetic tree prepared using the 16S rRNA gene, as well as the phylogenomic tree using the genome BLAST distance phylogeny method and 81 core housekeeping genes, respectively, showed that the closest relative of strain CWH03T was S. spongiicola HNM0071T. The average nucleotide identity and digital DNA-DNA hybridization values between strains CWH03T and S. spongiicola HNM0071T were 91.46% and 44.2%, respectively, which were below the thresholds of 96% and 70% for prokaryotic conspecific assignation. The G+C content of the genomic DNA of strain CWH03T was 72.3%. Whole-cell hydrolysates of strain CWH03T contained LL-diaminopimelic acid. The predominant menaquinone was MK-9(H8) (88.3%), and the major fatty acids were iso-C16:0 (28.4%), anteiso-C15:0 (15.0%) and iso-C15:0 (12.9%). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. Based on data obtained from phenotypic, phylogenetic, genomic, and chemotaxonomic analyses, strain CWH03T represents a novel species of the genus Streptomyces, for which the proposed name is Streptomyces pacificus sp. nov. The type strain is CWH03T ( = NBRC 114659T = TBRC 15780T).

CroSR391 , an ortholog of the λ Cro repressor, plays a major role in suppressing polVR391 -dependent mutagenesis

When subcloned into low-copy-number expression vectors, rumAB, encoding polVR391 (RumA'2 B), is best characterized as a potent mutator giving rise to high levels of spontaneous mutagenesis in vivo. This is in dramatic contrast to the poorly mutable phenotype when polVR391 is expressed from the native 88.5 kb R391, suggesting that R391 expresses cis-acting factors that suppress the expression and/or the activity of polVR391 . Indeed, we recently discovered that SetRR391 , an ortholog of λ cI repressor, is a transcriptional repressor of rumAB. Here, we report that CroSR391 , an ortholog of λ Cro, also serves as a potent transcriptional repressor of rumAB. Levels of RumA are dependent upon an interplay between SetRR391 and CroSR391 , with the greatest reduction of RumA protein levels observed in the absence of SetRR391 and the presence of CroSR391 . Under these conditions, CroSR391 completely abolishes the high levels of mutagenesis promoted by polVR391 expressed from low-copy-number plasmids. Furthermore, deletion of croSR391 on the native R391 results in a dramatic increase in mutagenesis, indicating that CroSR391 plays a major role in suppressing polVR391 mutagenesis in vivo. Inactivating mutations in CroSR391 therefore have the distinct possibility of increasing cellular mutagenesis that could lead to the evolution of antibiotic resistance of pathogenic bacteria harboring R391.

Alkaloids in Contemporary Drug Discovery to Meet Global Disease Needs

An overview is presented of the well-established role of alkaloids in drug discovery, the application of more sustainable chemicals, and biological approaches, and the implementation of information systems to address the current challenges faced in meeting global disease needs. The necessity for a new international paradigm for natural product discovery and development for the treatment of multidrug resistant organisms, and rare and neglected tropical diseases in the era of the Fourth Industrial Revolution and the Quintuple Helix is discussed.