A high-throughput, whole cell assay to identify compounds active against carbapenem-resistant Klebsiella pneumoniae

Innovative perspectives on the discovery of small molecule antibiotics

Antibiotics are essential to modern medicine, but multidrug-resistant (MDR) bacterial infections threaten their efficacy. Resistance evolution shortens antibiotic lifespans, limiting investment returns and slowing new approvals. Consequently, the WHO defines four innovation criteria: new chemical class, target, mode of action (MoA), and lack of cross-resistance. This review explores innovative discovery approaches, including AI-driven screening, metagenomics, and target-based strategies, to develop novel antibiotics that meet these criteria and combat MDR infections.

High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery

Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.

A Whole-Cell Assay for Detection of Antibacterial Activity in Actinomycete Culture Supernatants

Whole-cell antibacterial assays are particularly suitable for fast detection and semi-quantification of bioactivities in extracts or other solutions such as microbial culture supernatants. As Actinomycetales, including the members of the genus Streptomyces, are one of the most potent "suppliers" of antibiotics and other bioactive compounds, there is a strong interest in the development of useful assays enabling early identification of such valuable producers. Furthermore, such assays facilitate the screening of a large collection of clones for the detection of engineered "super-producers" that are essential for industrial manufacturing of the respective product.In this protocol, we describe a whole-cell assay for a fast detection of antimicrobial agents in culture supernatants. As model, Streptomyces fradiae DSM 41546, the producer of the antibiotic tylosin, and the test strain Bacillus subtilis ATCC 6051 are used. Culture supernatants of S. fradiae DSM 41546 and controls are diluted, and their antibiotic activity is tested against B. subtilis ATCC 6051. For the dilutions of tylosin-containing culture supernatant, a clear concentration-dependent growth inhibition effect on B. subtilis ATCC 6051 is demonstrated. In contrast, dilutions of the culture supernatant lacking tylosin do not inhibit the growth of B. subtilis. Moreover, including defined concentrations of tylosin facilitates the semi-quantification of tylosin in the culture supernatants.Our results confirm the applicability of the assay in fast screenings for antimicrobial products in culture supernatants. The protocol can be used as positive control within screening campaigns in the drug discovery field.

Overview on Strategies and Assays for Antibiotic Discovery

The increase in antibiotic resistance poses a major threat to global health. Actinomycetes, the Gram-positive bacteria of the order Actinomycetales, are fertile producers of bioactive secondary metabolites, including antibiotics. Nearly two-thirds of antibiotics that are used for the treatment of bacterial infections were originally isolated from actinomycetes strains belonging to the genus Streptomyces. This emphasizes the importance of actinomycetes in antibiotic discovery. However, the identification of a new antimicrobial compound and the exploration of its mode of action are very challenging tasks. Therefore, different approaches that enable the "detection" of an antibiotic and the characterization of the mechanisms leading to the biological activity are indispensable. Beyond bioinformatics tools facilitating the identification of biosynthetic gene clusters (BGCs), whole cell-screenings-in which cells are exposed to actinomycete-derived compounds-are a common strategy applied at the very early stage in antibiotic drug development. More recently, target-based approaches have been established. In this case, the drug candidates were tested for interactions with usually validated targets. This review focuses on the bioactivity-based screening methods and provides the readers with an overview on the most relevant assays for the identification of antibiotic activity and investigation of mechanisms of action. Moreover, the article includes examples of the successful application of these methods and suggestions for improvement.

Effects of Zinc Oxide Nanoparticles Synthesized Using Aspergillus niger on Carbapenem-Resistant Klebsiella pneumonia In Vitro and In Vivo

Currently, the mortality rate in Saudi Arabia's ICUs is increasing due to the spread of Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria. This study was carried out to evaluate the ability of biologically synthesized zinc oxide nanoparticles (ZnO-NPs) using Aspergillus niger to overcome carbapenem-resistant K. pneumoniae (KPC) in vitro and in vivo. ZnO-NPs were synthesized via a biological method and characterized using UV-Vis spectroscopy, Zetasizer and zeta potential analyses, x-ray diffraction spectroscopy, Fourier transform infrared spectroscopy, scanning electron microscopy (SEM), and energy-dispersive x-ray spectroscopy (EDX). In vitro sensitivity of KPC to ZnO-NPs was identified using the well diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined by a macro-dilution method. The morphological alteration of KPC cells after ZnO-NPs treatment was observed by SEM. The in vivo susceptibility of KPC cells to ZnO-NPs ointment was evaluated using wound healing in experimental rats. The chemical characterization findings showed the formation, stability, shape, and size of the synthesized nanoparticles. The MIC and MBC were 0.7 and 1.8 mg/ml, respectively. The in vivo results displayed reduced inflammation and wound re-epithelialization of KPC-infected rats. These findings demonstrated that ZnO-NPs have great potential to be developed as antibacterial agents.

Biosynthesis of Zinc Oxide Nanoparticles from Acacia nilotica (L.) Extract to Overcome Carbapenem-Resistant Klebsiella Pneumoniae

Recently, concerns have been raised globally about antimicrobial resistance, the prevalence of which has increased significantly. Carbapenem-resistant Klebsiella pneumoniae (KPC) is considered one of the most common resistant bacteria, which has spread to ICUs in Saudi Arabia. This study was established to investigate the antibacterial activity of biosynthesized zinc oxide nanoparticles (ZnO-NPs) against KPC in vitro and in vivo. In this study, we used the aqueous extract of Acacia nilotica (L.) fruits to mediate the synthesis of ZnO-NPs. The nanoparticles produced were characterized by UV-vis spectroscopy, zetasizer and zeta potential analyses, X-ray diffraction (XRD) spectroscopy, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and transmission electron microscopy (TEM). The antimicrobial activity of ZnO-NPs against KPC was determined via the well diffusion method, and determining minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC), the results showed low MIC and MBC when compared with the MIC and MBC of Imipenem and Meropenem antibiotics. The results of in vitro analysis were supported by the results upon applying ZnO-NP ointment to promote wound closure of rats, which showed better wound healing than the results with imipenem ointment. The biosynthesized ZnO-NPs showed good potential for use against bacteria due to their small size, applicability, and low toxicity to human cells.