Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro

Multi-drug strategies have been attempted to prolong the efficacy of existing antibiotics, but with limited success. Here we show that the evolution of multi-drug-resistant Escherichia coli can be manipulated in vitro by administering pairs of antibiotics and switching between them in ON/OFF manner. Using a multiplexed cell culture system, we find that switching between certain combinations of antibiotics completely suppresses the development of resistance to one of the antibiotics. Using this data, we develop a simple deterministic model, which allows us to predict the fate of multi-drug evolution in this system. Furthermore, we are able to reverse established drug resistance based on the model prediction by modulating antibiotic selection stresses. Our results support the idea that the development of antibiotic resistance may be potentially controlled via continuous switching of drugs

Determination of the Primary Molecular Target of 1,2,4-Triazole-Ciprofloxacin Hybrids

We have synthesized and examined the antibacterial activity, toxicity and affinity towards bacterial type II topoisomerases of a series of 1,2,4-triazole-ciprofloxacin hybrids. A number of these compounds displayed enhanced activity against Gram-positive and Gram-negative bacteria when compared to ciprofloxacin. The toxic concentrations of the obtained derivatives, evaluated on HEK-293 cells using MTT assay, were much higher than concentrations required to produce antibacterial effect. Finally, the results of enzymatic studies showed that the analyzed compounds demonstrated other preferences as regards primary and secondary molecular targets than ciprofloxacin.This research was supported by the Ministry of Science and Higher Education under Iuventus Plus grant No. IP2014 037473. Tomasz Plech is a recipient of the Fellowship for Young Researchers with Outstanding Scientific Achievements from the Medical University of Lublin (Lublin, Poland)

Strategies to prevent the occurrence of resistance against antibiotics by using advanced materials

This is a post-peer-review, pre-copyedit version of an article published in Applied microbiology and biotechnology The final authenticated version is available online at: http://dx.doi.org/10.1007/s00253-018-8776-0Drug resistance occurrence is a global healthcare concern responsible for the increased morbidity and mortality in hospitals, time of hospitalisation and huge financial loss. The failure of the most antibiotics to kill Bsuperbugs^ poses the urgent need to develop innovative strategies aimed at not only controlling bacterial infection but also the spread of resistance. The prevention of pathogen host invasion by inhibiting bacterial virulence and biofilm formation, and the utilisation of bactericidal agents with different mode of action than classic antibiotics are the two most promising new alternative strategies to overcome antibiotic resistance. Based on these novel approaches, researchers are developing different advanced materials (nanoparticles, hydrogels and surface coatings) with novel antimicrobial properties. In this review, we summarise the recent advances in terms of engineered materials to prevent bacteria-resistant infections according to the antimicrobial strategies underlying their design.Peer ReviewedPostprint (author's final draft

Impacts of pathogen-host-drug interaction in the evolution and spread of antimicrobial-resistant pathogens

Background: The single antibiotic drug monotherapies have been used by clinicians in medical treatments of various infectious diseases including tuberculosis (TB); however, World Health Organization accredited the rise of antimicrobial resistant bacterial pathogens, is a major global health crisis. As a result, a widely promising strategy known as antibiotic drug combination therapies have been designed to combat the evolution of drug-resistant pathogens, to enhance the current treatment efficacy by combining more than two antibiotic drugs, and for the efficient treatment of numerous infectious diseases including TB, HIV/AIDS, malaria. However, the disease-causing pathogens became resistant to multiple antibiotic drugs and can no longer be destroyed. One of the influencing factors of antibiotic drug combination treatment success failure is pathogen-host-antibiotic interaction which affect the combined drug outcomes and may influence evolution of multidrug-resistant strains. In such context, the main objective of this review paper was to assess the impacts of pathogen-host-antibiotic interaction in the evolution and spread of multi-drug resistant pathogens against drug-combination therapy. Understanding the potential mechanisms of drug-drug, host-antibiotic and host-pathogen interactions help to inform decisions as to set-up in clinical settings in order to limit the evolution and spread of multi- drug resistant bacterial strains. Most significantly, in the near future sustainable bacterial infection therapies for potential adaptive pathogens include synergy-based drug combination and host-directed therapies in drug combination could be exercised to tackle the multi-drug resistance crisis by enhancing the combined drug treatment efficacy and prevent bacteria adapting to combination treatments

Evaluation of NAD(+)-dependent DNA ligase of mycobacteria as a potential target for antibiotics

Mycobacteria contain genes for several DNA ligases, including ligA, which encodes a NAD+-dependent enzyme that has been postulated to be a target for novel antibacterial compounds. Using a homologous recombination system, direct evidence is presented that wild-type ligA cannot be deleted from the chromosome of Mycobacterium smegmatis. Deletions of native ligA in M. smegmatis could be obtained only after the integration of an extra copy of M. smegmatis or Mycobacterium tuberculosis ligA into the attB site of the chromosome, with expression controlled by chemically inducible promoters. The four ATP-dependent DNA ligases encoded by the M. smegmatis chromosome were unable to replace the function of LigA. Interestingly, the LigA protein from M. smegmatis could be substituted with the NAD+-dependent DNA ligase of Escherichia coli or the ATP-dependent ligase of bacteriophage T4. The conditional mutant strains allowed the analysis of the effect of LigA depletion on the growth of M. smegmatis. The protein level of the conditional mutants was estimated by Western blot analysis using antibodies raised against LigA of M. tuberculosis. This revealed that a strong overproduction or depletion of LigA did not affect the growth or survival of mycobacteria under standard laboratory conditions. In conclusion, although NAD+-dependent DNA ligase is essential for mycobacterial viability, only low levels of protein are required for growth. These findings suggest that very efficient inhibition of enzyme activity would be required if NAD+-dependent DNA ligase is to be useful as an antibiotic target in mycobacteria. The strains developed here will provide useful tools for the evaluation of the efficacy of any appropriate compounds in mycobacteria

Coleopteran Antimicrobial Peptides: Prospects for Clinical Applications

Antimicrobial peptides (AMPs) are activated in response to septic injury and have important roles in vertebrate and invertebrate immune systems. AMPs act directly against pathogens and have both wound healing and antitumor activities. Although coleopterans comprise the largest and most diverse order of eukaryotes and occupy an earlier branch than Drosophila in the holometabolous lineage of insects, their immune system has not been studied extensively. Initial research reports, however, indicate that coleopterans possess unique immune response mechanisms, and studies of these novel mechanisms may help to further elucidate innate immunity. Recently, the complete genome sequence of Tribolium was published, boosting research on coleopteran immunity and leading to the identification of Tribolium AMPs that are shared by Drosophila and mammals, as well as other AMPs that are unique. AMPs have potential applicability in the development of vaccines. Here, we review coleopteran AMPs, their potential impact on clinical medicine, and the molecular basis of immune defense

The pharmacokinetic–pharmacodynamic modelling framework as a tool to predict drug resistance evolution

Pharmacokinetic–pharmacodynamic (PKPD) models, which describe how drug concentrations change over time and how that affects pathogen growth, have proven highly valuable in designing optimal drug treatments aimed at bacterial eradication. However, the fast rise of antimicrobial resistance calls for increased focus on an additional treatment optimization criterion: avoidance of resistance evolution. We demonstrate here how coupling PKPD and population genetics models can be used to determine treatment regimens that minimize the potential for antimicrobial resistance evolution. Importantly, the resulting modelling framework enables the assessment of resistance evolution in response to dynamic selection pressures, including changes in antimicrobial concentration and the emergence of adaptive phenotypes. Using antibiotics and antimicrobial peptides as an example, we discuss the empirical evidence and intuition behind individual model parameters. We further suggest several extensions of this framework that allow a more comprehensive and realistic prediction of bacterial escape from antimicrobials through various phenotypic and genetic mechanisms

In silico generation of novel, drug-like chemical matter using the LSTM neural network

The exploration of novel chemical spaces is one of the most important tasks of cheminformatics when supporting the drug discovery process. Properly designed and trained deep neural networks can provide a viable alternative to brute-force de novo approaches or various other machine-learning techniques for generating novel drug-like molecules. In this article we present a method to generate molecules using a long short-term memory (LSTM) neural network and provide an analysis of the results, including a virtual screening test. Using the network one million drug-like molecules were generated in 2 hours. The molecules are novel, diverse (contain numerous novel chemotypes), have good physicochemical properties and have good synthetic accessibility, even though these qualities were not specific constraints. Although novel, their structural features and functional groups remain closely within the drug-like space defined by the bioactive molecules from ChEMBL. Virtual screening using the profile QSAR approach confirms that the potential of these novel molecules to show bioactivity is comparable to the ChEMBL set from which they were derived. The molecule generator written in Python used in this study is available on request.Comment: in this version fixed some reference number

Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa

<p>Abstract</p> <p>Background</p> <p>The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus.</p> <p>Results</p> <p>In this study we demonstrate that pooled sequencing is applicable for the analysis of sequence variations of strain collections with more than 10 individual isolates. Pooled sequencing of 36 clinical <it>Pseudomonas aeruginosa </it>isolates revealed that essential and highly expressed proteins evolve at lower rates, whereas extracellular proteins evolve at higher rates. We furthermore refined the list of experimentally essential <it>P. aeruginosa </it>genes, and identified 980 genes that show no sequence variation at all. Among the conserved nonessential genes we found several that are involved in regulation, motility and virulence, indicating that they represent factors of evolutionary importance for the lifestyle of a successful environmental bacterium and opportunistic pathogen.</p> <p>Conclusion</p> <p>The detailed analysis of a comprehensive set of <it>P. aeruginosa </it>genomes in this study clearly disclosed detailed information of the genomic makeup and revealed a large set of highly conserved genes that play an important role for the lifestyle of this microorganism. Sequencing strain collections enables for a detailed and extensive identification of sequence variations as potential bacterial adaptation processes, e.g., during the development of antibiotic resistance in the clinical setting and thus may be the basis to uncover putative targets for novel treatment strategies.</p