Designing drugs that overcome antibacterial resistance: where do we stand and what should we do?

Antisense and Functional Nucleic Acids in Rational Drug Development

This review is focused on antisense and functional nucleic acid used for completely rational drug design and drug target assessment, aiming to reduce the time and money spent and increase the successful rate of drug development. Nucleic acids have unique properties that play two essential roles in drug development as drug targets and as drugs. Drug targets can be messenger, ribosomal, non-coding RNAs, ribozymes, riboswitches, and other RNAs. Furthermore, various antisense and functional nucleic acids can be valuable tools in drug discovery. Many mechanisms for RNA-based control of gene expression in both pro-and-eukaryotes and engineering approaches open new avenues for drug discovery with a critical role. This review discusses the design principles, applications, and prospects of antisense and functional nucleic acids in drug delivery and design. Such nucleic acids include antisense oligonucleotides, synthetic ribozymes, and siRNAs, which can be employed for rational antibacterial drug development that can be very efficient. An important feature of antisense and functional nucleic acids is the possibility of using rational design methods for drug development. This review aims to popularize these novel approaches to benefit the drug industry and patients.

General and Specific Cytotoxicity of Chimeric Antisense Oligonucleotides in Bacterial Cells and Human Cell Lines

In the last two decades, antisense oligonucleotide technology has emerged as a promising approach to tackling various healthcare issues and diseases, such as antimicrobial resistance, cancer, and neurodegenerative diseases. Despite the numerous improvements in the structure and modifications of the antisense oligonucleotides (ASOs), there are still specific problems with their clinical efficacy and preclinical cytotoxicity results. To better understand the effects of the ASOs in this paper, we conducted many MTT assays to assess the general and specific cytotoxicity of four new chimeric ASOs in bacterial cells and human cell lines. We demonstrate the absence of inhibitory activity in the human pathogenic bacteria Staphylococcus aureus by non-specific ASOs. The pVEC-ASO1 and pVEC-ASO2 are designed to have no specific targets in S. aureus. They have only partial hybridization to the guanylate kinase mRNA. The pVEC-ASO3 targets UBA2 mRNA, a hallmark cancer pathology in MYC-driven cancer, while pVEC-ASO4 has no complementary sequences. We discovered some cytotoxicity of the non-specific ASOs in healthy and cancer human cell lines. The results are compared with two other ASOs, targeting specific mRNA in cancer cells. All ASOs are delivered into the cell via the cell-penetrating oligopeptide pVEC, which is attached to them. We draw a good correlation between the thermodynamic stability of ASO/target RNA and the toxicity effect in human cell lines. The data obtained signify the importance of thorough bioinformatic analysis and high specificity in designing and developing novel ASOs for safer therapeutic agents in clinical practice.

The Next Generation of Drug Delivery: Harnessing the Power of Bacteriophages

The use of biomaterials, such as bacteriophages, as drug delivery vehicles (DDVs) has gained increasing interest in recent years due to their potential to address the limitations of conventional drug delivery systems. Bacteriophages offer several advantages as drug carriers, such as high specificity for targeting bacterial cells, low toxicity, and the ability to be engineered to express specific proteins or peptides for enhanced targeting and drug delivery. In addition, bacteriophages have been shown to reduce the development of antibiotic resistance, which is a major concern in the field of antimicrobial therapy. Many initiatives have been taken to take up various payloads selectively and precisely by surface functionalization of the outside or interior of self-assembling viral protein capsids. Bacteriophages have emerged as a promising platform for the targeted delivery of therapeutic agents, including drugs, genes, and imaging agents. They possess several properties that make them attractive as drug delivery vehicles, including their ability to specifically target bacterial cells, their structural diversity, their ease of genetic manipulation, and their biocompatibility. Despite the potential advantages of using bacteriophages as drug carriers, several challenges and limitations need to be addressed. One of the main challenges is the limited host range of bacteriophages, which restricts their use to specific bacterial strains. However, this can also be considered as an advantage, as it allows for precise and targeted drug delivery to the desired bacterial cells. The use of biomaterials, including bacteriophages, as drug delivery vehicles has shown promising potential to address the limitations of conventional drug delivery systems. Further research is needed to fully understand the potential of these biomaterials and address the challenges and limitations associated with their use.

Ameliorating Gonorrhea: Recent Therapeutic Adaptations and Scope to Improve its Prevailing Condition

BACKGROUND

Gonorrhea is a sexually transmitted infection (STI) caused by the bacteria Neisseria gonorrhoeae. According to recent research, the prevalence of gonorrhea has been increasing in many parts of the world, with some areas reporting high rates of antibiotic resistance. In the United States, the Centers for Disease Control and Prevention (CDC) reported that the number of reported gonorrhea cases increased by 56% between 2015 and 2019. Globally, the World Health Organization (WHO) estimated that there were 87 million new cases of gonorrhea in 2016, with the highest burden of infection in low- and middle-income countries. Research has also shown that gonorrhea is becoming increasingly resistant to conventional antibiotics, increasing the prevalence of gonorrhea. This raises concerns and challenges in disease management.

OBJECTIVES

The present review gives updated insight on the current state of the disease, challenges, and shortcomings of existing approaches along with the modern and alternative direction like vaccine development, its challenges, and scope to confront the existing state of drug resistance and increased rate of incidence. Alternative strategies like immunotherapy and phage therapy along with recent antibiotics researched for the treatment of gonorrhea.

CONCLUSION

The review provides a thorough insight into the current state of the disease and various available methods used currently and recommended by WHO. To overcome disease prevalence, various alternate therapies are coming into the limelight. However, scientists and researchers show a lack of interest in the drug development and research of gonorrhea, due to less commercial scope, lack of funding, and limited scope in the scientific scenario. These hurdles need to be overcome to meet the WHO vision of reducing gonorrhea by 90% by 2030. So, there is a need to optimize the drug therapy (optimizing dosing schedule, and precision monitoring) to reduce the chance of drug resistance. Also, there is a wide scope for drug and therapeutic system development.

Targeting FMN, TPP, SAM-I, and glmS Riboswitches with Chimeric Antisense Oligonucleotides for Completely Rational Antibacterial Drug Development

Antimicrobial drug resistance has emerged as a significant challenge in contemporary medicine due to the proliferation of numerous bacterial strains resistant to all existing antibiotics. Meanwhile, riboswitches have emerged as promising targets for discovering antibacterial drugs. Riboswitches are regulatory elements in certain bacterial mRNAs that can bind to specific molecules and control gene expression via transcriptional termination, prevention of translation, or mRNA destabilization. By targeting riboswitches, we aim to develop innovative strategies to combat antibiotic-resistant bacteria and enhance the efficacy of antibacterial treatments. This convergence of challenges and opportunities underscores the ongoing quest to revolutionize medical approaches against evolving bacterial threats. For the first time, this innovative review describes the rational design and applications of chimeric antisense oligonucleotides as antibacterial agents targeting four riboswitches selected based on genome-wide bioinformatic analyses. The antisense oligonucleotides are coupled with the cell-penetrating oligopeptide pVEC, which penetrates Gram-positive and Gram-negative bacteria and specifically targets glmS, FMN, TPP, and SAM-I riboswitches in Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli. The average antibiotic dosage of antisense oligonucleotides that inhibits 80% of bacterial growth is around 700 nM (4.5 μg/mL). Antisense oligonucleotides do not exhibit toxicity in human cell lines at this concentration. The results demonstrate that these riboswitches are suitable targets for antibacterial drug development using antisense oligonucleotide technology. The approach is fully rational because selecting suitable riboswitch targets and designing ASOs that target them are based on predefined criteria. The approach can be used to develop narrow or broad-spectrum antibiotics against multidrug-resistant bacterial strains for a short time. The approach is easily adaptive to new resistance using targeting NGS technology.

Structural Study of Potent Triazole-Based Inhibitors of Staphylococcus aureus Biotin Protein Ligase

The rise of multidrug-resistant bacteria, such as Staphylococcus aureus, has highlighted global urgency for new classes of antibiotics. Biotin protein ligase (BPL), a critical metabolic regulatory enzyme, is an important target that shows significant promise in this context. Here we report the in silico docking, synthesis, and biological assay of a new series of N1-diphenylmethyl-1,2,3-triazole-based S. aureus BPL (SaBPL) inhibitors (8-19) designed to probe the adenine binding site and define whole-cell activity for this important class of inhibitor. Triazoles 13 and 14 with N1-propylamine and -butanamide substituents, respectively, were particularly potent with K i values of 10 ± 2 and 30 ± 6 nM, respectively, against SaBPL. A strong correlation was apparent between the K i values for 8-19 and the in silico docking, with hydrogen bonding to amino acid residues S128 and N212 of SaBPL likely contributing to potent inhibition.

Targeting SAM-I Riboswitch Using Antisense Oligonucleotide Technology for Inhibiting the Growth of Staphylococcus aureus and Listeria monocytogenes

With the discovery of antibiotics, a productive period of antibacterial drug innovation and application in healthcare systems and agriculture resulted in saving millions of lives. Unfortunately, the misusage of antibiotics led to the emergence of many resistant pathogenic strains. Some riboswitches have risen as promising targets for developing antibacterial drugs. Here, we describe the design and applications of the chimeric antisense oligonucleotide (ASO) as a novel antibacterial agent. The pVEC-ASO-1 consists of a cell-penetrating oligopeptide known as pVEC attached to an oligonucleotide part with modifications of the first and the second generations. This combination of modifications enables specific mRNA degradation under multiple turnover conditions via RNase H. The pVEC-ASO targets the S-adenosyl methionine (SAM)-I riboswitch found in the genome of many Gram-positive bacteria. The SAM-I riboswitch controls not only the biosynthesis but also the transport of SAM. We have established an antibiotic dosage of 700 nM (4.5 µg/mL) of pVEC-ASO that inhibits 80% of the growth of Staphylococcus aureus and Listeria monocytogenes. The pVEC-ASO-1 does not show any toxicity in the human cell line at MIC80's concentration. We have proven that the SAM-I riboswitch is a suitable target for antibacterial drug development based on ASO. The approach is rational and easily adapted to other bacterial RNA targets.

Targeting TPP Riboswitches Using Chimeric Antisense Oligonucleotide Technology for Antibacterial Drug Development

Nowadays, the emergence and the transmission of multidrug-resistant pathogenic bacteria are a severe menace mounting a lot of pressure on the healthcare systems worldwide. Many severe outbreaks of bacterial infections have been reported worldwide in recent years. Thus, there is an immediate demand to develop antibiotics. Some riboswitches are potential targets for overcoming bacterial resistance. This paper demonstrates the bacteriostatic effect of an antisense oligonucleotide (ASO) engineered to suppress the growth of pathogenic bacteria such as Listeria monocytogenes by targeting the Thiamine Pyrophosphate (TPP) riboswitch. It does not inhibit the growth of the conditional pathogenic bacteria Escherichia coli, as it lacks the TPP riboswitch, showing the specificity of action of our ASO. It is covalently bonded with the cell-penetrating protein pVEC. We did bioinformatics analyses of the thiamine pyrophosphate riboswitch regarding its role in synthesizing the metabolite thiamine pyrophosphate, which is essential for bacteria. L. monocytogenes is intrinsically resistant to cephalosporins and usually is treated with ampicillin. A dosage of ASO has been established that inhibits 80% of bacterial growth at 700 nM (4.5 μg/mL). Thus, the TPP riboswitch is a valuable antibacterial target.

Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets

Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.

Engineering Antisense Oligonucleotides as Antibacterial Agents That Target FMN Riboswitches and Inhibit the Growth of Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli

In the past several decades, antibiotic drug resistance has emerged as a significant challenge in modern medicine due to the rise of many bacterial pathogenic strains resistant to all known antibiotics. At the same time, riboswitches have emerged as novel targets for antibacterial drug discovery. Here for the first time, we describe the design and applications of antisense oligonucleotides as antibacterial agents that target a riboswitch. The antisense oligonucleotides are covalently coupled with two different cell-penetrating peptides, penetrating Gram-positive and Gram-negative bacterial cells. We specifically target Flavin MonoNucleotide (FMN) riboswitches in Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli that control both synthesis and import of FMN precursors. We have established an average antibiotic dosage by antisense oligonucleotides that inhibit 80% of bacterial growth at 700 nM (4.5 μg/mL). Furthermore, the antisense oligonucleotides do not exhibit toxicity in human cell lines at this concentration. The results demonstrate that riboswitches are suitable targets in antisense technology for antibacterial drug development.

Amphipathic dendritic poly-peptides carrier to deliver antisense oligonucleotides against multi-drug resistant bacteria in vitro and in vivo

Background

Outbreaks of infection due to multidrug-resistant (MDR) bacteria, especially Gram-negative bacteria, have become a global health issue in both hospitals and communities. Antisense oligonucleotides (ASOs) based therapeutics hold a great promise for treating infections caused by MDR bacteria. However, ASOs therapeutics are strangled because of its low cell penetration efficiency caused by the high molecular weight and hydrophilicity.

Results

Here, we designed a series of dendritic poly-peptides (DPP1 to DPP12) to encapsulate ASOs to form DSPE-mPEG2000 decorated ASOs/DPP nanoparticles (DP-AD1 to DP-AD12) and observed that amphipathic DP-AD2, 3, 7 or 8 with a positive charge ≥ 8 showed great efficiency to deliver ASOs into bacteria, but only the two histidine residues contained DP-AD7 and DP-AD8 significantly inhibited the bacterial growth and the targeted gene expression of tested bacteria in vitro. DP-AD7_anti-acpP remarkably increased the survival rate of septic mice infected by ESBLs-E. coli, exhibiting strong antibacterial effects in vivo.

Conclusions

For the first time, we designed DPP as a potent carrier to deliver ASOs for combating MDR bacteria and demonstrated the essential features, namely, amphipathicity, 8–10 positive charges, and 2 histidine residues, that are required for efficient DPP based delivery, and provide a novel approach for the development and research of the antisense antibacterial strategy.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01384-y.

Perspectives of physicians and pharmacists on rational use of antibiotics in Turkey and among Turkish migrants in Germany, Sweden and the Netherlands: a qualitative study

Background

Antimicrobial resistance may result from inappropriate use of antibiotics in health care. Turkey is one of the countries with the highest antibiotic consumption in the world. Considering the role of transnational ties between Turkish migrants and their social contacts in Turkey, the attitudes and behaviors relating to rational antibiotic use in Turkey can also affect the use of antibiotics by Turkish migrants residing abroad. This study explores physicians’ and pharmacists’ experiences and perspectives on rational antibiotic use among Turkish adults in Turkey and among Turkish migrants in Germany, Sweden, and the Netherlands, three European countries with large populations of Turkish migrants.

Methods

Following a qualitative study design using convenience and snowball sampling, in-depth interviews with 21 family physicians and 24 pharmacists were conducted in the aforementioned countries. We transcribed all interviews verbatim and performed content analysis separately in the countries, followed by translation, pooling and joint interpretation of the findings.

Results

Physicians and pharmacists encountered irrational use of antibiotics among their patients in Turkey. Physicians interviewed in the three European countries explained that Turkish migrants differ from non-migrants with respect to their attitudes towards antibiotics, for example by more often expecting to be prescribed antibiotics. All physicians and pharmacists in the selected countries reported to inform their patients on how to use antibiotics upon prescription; however, Turkish migrants’ poor language proficiency was considered as a substantial communication barrier by the physicians and pharmacists interviewed in the European countries.

Conclusions

The study illustrated some aspects of irrational antibiotic use among the population in Turkey and Turkish migrants in selected European countries. It emphasized the need for closer community participation, adequate information campaigns, as well as in-service training of health care providers in Turkey. The strategies and interventions on rational antibiotic use should also be supported and encouraged by health care providers, who need to reach out to people with various cultural backgrounds.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12875-022-01636-8.

Targeting glmS Ribozyme with Chimeric Antisense Oligonucleotides for Antibacterial Drug Development

Due to the steady rise of multidrug-resistant pathogenic bacteria worldwide, it is critical to develop novel antibacterial drugs. This article presents chimeric antisense oligonucleotides that inhibit the bacterial growth of Staphylococcus aureus, one of the most frequent causes of hospital-acquired infections. The chimeric antisense oligonucleotides have a combination of first- and second-generation chemical modification. To deliver the antisense oligonucleotides into a cell, we apply a cell-penetrating oligopeptide attached to them. We have performed complete bioinformatics analyses of the glmS ribozyme present in S. aureus and its essential role in the biochemical pathway of glucosamine-6-phosphate synthesis. Besides, we have analyzed the bacteria for alternative metabolic pathways, such as the nagA gene. The first antisense oligonucleotide explicitly targets the glmS riboswitch, while the second explicitly targets the nagA mRNA. We have evaluated that combined, the antisense oligonucleotides block the synthesis of glucosamine-6-phosphate entirely and inhibit the bacterial growth of S. aureus. However, the glmS riboswitch targeting the antisense oligonucleotide is sufficient to inhibit the growth of S. aureus with a MIC80 of 5 μg/mL. The glmS ribozyme is a very suitable target for antibacterial drug development with antisense oligonucleotides.

Synthesis, anti-microbial, toxicity and molecular docking studies of N-nitroso-N-phenylhydroxylamine (cupferron) and its derivatives

Bacterial resistance to antimicrobial agents is increasing at an alarming rate globally and requires new lead compounds for antibiotics. In this study, N-phenyl-N-nitroso hydroxylamine (cupferron) and its derivatives have been synthesised using readily available starting materials. The compounds were obtained in high yield and purity. They show activity towards a range of Gram-positive and Gram-negative pathogenic bacteria, with minimum inhibitory concentration (MIC) values as low as 2 μg.mL^-1 against the tested organisms, especially for Gram-positive species. Toxicity studies on the lead compound 3b indicate insignificant effects on healthy cell lines. Molecular docking studies on the lead compound identify possible binding modes of the compound, and the results obtained correlate with those of in vitro and MIC studies. The lead compound shows excellent drug-likeness properties.

RSwitch: A Novel Bioinformatics Database on Riboswitches as Antibacterial Drug Targets

The RSwitch is a MySQL database implemented on a PHP-based server, which also provides various useful tools for analyses of DNA, RNA, and protein sequences applying a user-friendly interface. The RSwitch database currently contains information and annotations of 215 bacterial riboswitches from 16 different types found in 50 human pathogenic bacteria. The riboswitch classes include those sensing FMN, glmS, Cobalamin, Lysine, SAH, SAM, Purine, TPP, c-di-GMPI, c-di-GMPII, Moco, PreQ1, Fluoride, Glycine, Mg²⁺, and Mn²⁺ type of bacterial riboswitches. The database provides information about the riboswitch aptamer sequences, the thermodynamic ensemble of the RNA structures on partition function and on free minimum energy function. Additionally, the database presents the centroid structure and the positional entropy for each position of the aptamer sequences. The database also provides the biochemical pathways in which the riboswitches are involved in, as well as multiple sequence alignments, multi-drug resistance bacterial strains and consensus motifs for each type of the switches. The RSwitch database is permanently available online without any restrictions. This bioinformatics database provides for the first time all information needed for assessing the suitability of the presented riboswitches as antibacterial drug targets.

Polyphenols against infectious diseases: Controlled release nano-formulations

The emergence of multi-drug resistant (MDR) pathogens has become a global threat and a cause of significant morbidity and mortality around the world. Natural products have been used as a promising approach to counter the infectious diseases associated with these pathogens. The application of natural products and their derivatives especially polyphenolic compounds as antibacterial agents is an active area of research, and prior studies have successfully treated a variety of bacterial infections using these polyphenolic compounds. However, delivery of polyphenolic compounds has been challenging due to their physicochemical properties and often poor aqueous solubility. In this regard, nanotechnology-based novel drug delivery systems offer many advantages, including improving bioavailability and the controlled release of polyphenolic compounds. This review summarizes the pharmacological mechanism and use of nano-formulations in developing controlled release delivery systems of naturally occurring polyphenols in infectious diseases.

Non-hydroxamate inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): A critical review and future perspective

1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the second step of the non-mevalonate (or MEP) pathway that functions in several organisms and plants for the synthesis of isoprenoids. DXR is essential for the survival of multiple pathogenic bacteria/parasites, including those that cause tuberculosis and malaria in humans. DXR function is inhibited by fosmidomycin (1), a natural product, which forms a chelate with the active site divalent metal (Mg²⁺/Mn²⁺) through its hydroxamate metal-binding group (MBG). Most of the potent DXR inhibitors are structurally similar to 1 and retain hydroxamate despite the unfavourable pharmacokinetic and toxicity profile of the latter. We provide our perspective on the lack of non-hydroxamate DXR inhibitors. We also highlight the fundamental flaws in the design of MBG in these molecules, primarily responsible for their failure to inhibit DXR. We also suggest that for designing next-generation non-hydroxamate DXR inhibitors, approaches followed for other metalloenzymes targets may be exploited.

Strategies for recombinant production of antimicrobial peptides with pharmacological potential

INTRODUCTION

The need to develop new drugs for the control of pathogenic microorganisms has redoubled efforts to prospect for antimicrobial peptides (AMPs) from natural sources and to characterize its structure and function. These molecules present a broad spectrum of action against different microorganisms and frequently present promiscuous action, with anticancer and immunomodulatory activities. Furthermore, AMPs can be used as biopharmaceuticals in the treatment of hospital-acquired infections and other serious diseases with relevant social and economic impacts.Areas covered: The low yield and the therefore difficult extraction and purification process in AMPs are problems that limit their industrial application and scientific research. Thus, optimized heterologous expression systems were developed to significantly boost AMP yields, allow high efficiency in purification and structural optimization for the increase of therapeutic activity.Expert opinion: This review provides an update on recent developments in the recombinant production of ribosomal and non-ribosomal synthesis of AMPs and on strategies to increase the expression of genes encoding AMPs at the transcriptional and translational levels and regulation of the post-translational modifications. Moreover, there are detailed reports of AMPs that have already reached marketable status or are in the pipeline under advanced stages of preclinical testing.

An African perspective on the prevalence, fate and effects of carbapenem resistance genes in hospital effluents and wastewater treatment plant (WWTP) final effluents: A critical review

This article provides an overview of the antibiotic era and discovery of earliest antibiotics until the present day state of affairs, coupled with the emergence of carbapenem-resistant bacteria. The ways of response to challenges of antibiotic resistance (AR) such as the development of novel strategies in the search of new antibiotics, designing more effective preventive measures as well as the ecology of AR have been discussed. The applications of plant extract and chemical compounds like nanomaterials which are based on recent developments in the field of antimicrobials, antimicrobial resistance (AMR), and chemotherapy were briefly discussed. The agencies responsible for environmental protection have a role to play in dealing with the climate crisis which poses an existential threat to the planet, and contributes to ecological support towards pathogenic microorganisms. The environment serves as a reservoir and also a vehicle for transmission of antimicrobial resistance genes hence, as dominant inhabitants we have to gain a competitive advantage in the battle against AMR.

What we can do? The risk factors for multi-drug resistant infection in pediatric intensive care unit (PICU): a case-control study

Background

The risk factors for multi-drug resistant infection (MDRI) in the pediatric intensive care unit (PICU) remain unclear. It’s necessary to evaluate the epidemiological characteristics and risk factors for MDRI in PICU, to provide insights into the prophylaxis of MDRI clinically.

Methods

Clinical data of 79 PICU children with MDRI were identified, and 80 children in PICU without MDRI in the same period were selected as control group. The related children’s characteristics, clinical care, microbiologic data, treatments provided, and outcomes of the patients with were reviewed and collected. Univariate and multivariate logistic regression analyses were performed to identify the potential risks of MDRI in PICU.

Results

Of the diagnosed 79 cases of MDRI, there were28 cases of CR-AB, 24 cases of MRSA, 22 cases of PDR-PA,3 cases of VRE and 2 cases of CRE respectively. Univariate analyses indicated that the length of PICU stay, the duration of mechanical ventilation > 5 days, parenteral nutrition, coma, urinary catheter indwelling, invasive operation, 2 or more antibiotics use were associated with MDRIs (all p < 0.05); The logistic multiple regression analyses indicated that coma, parenteral nutrition, 2 or more antibiotics use and the duration of mechanical ventilation > 5 days were independent risk factors associated with MDRI (all p < 0.05).

Conclusions

This present study has identified several potentially modifiable risk factors for MDRI in PICU, it’s conducive to take appropriate measures targeting risk factors of MDRI for health care providers to reduce MDRI.

A New Antisense Phosphoryl Guanidine Oligo-2'-O-Methylribonucleotide Penetrates Into Intracellular Mycobacteria and Suppresses Target Gene Expression

The worldwide spread of multidrug-resistant Mycobacterium tuberculosis strains prompted the development of new strategies to combat tuberculosis, one of which is antisense therapy based on targeting bacterial mRNA by oligonucleotide derivatives. However, the main limitation of antisense antibacterials is poor cellular uptake because of electrostatic charge. Phosphoryl guanidine oligo-2′-O-methylribonucleotides (2′-OMe PGOs) are a novel type of uncharged RNA analogues with high RNA affinity, which penetrate through the bacterial cell wall more efficiently. In this study, we investigated the uptake and biological effects of 2′-OMe PGO in mycobacteria. The results indicated that 2′-OMe PGO specific for the alanine dehydrogenase-encoding ald gene inhibited the growth of Mycobacterium smegmatis and downregulated ald expression at both the transcriptional and translational levels through an RNase H-independent mechanism, showing higher biological activity than its phosphorothioate oligonucleotide counterpart. Confocal microscopy revealed that the anti-ald 2′-OMe PGO was taken up by intracellular mycobacteria residing in RAW 264.7 macrophages without exerting toxic effects on eukaryotic cells, indicating that 2′-OMe PGO was able to efficiently cross two cellular membranes. In addition, 2′-OMe PGO inhibited the transcription of the target ald gene in M. smegmatis-infected macrophages. Thus, we demonstrated, for the first time, a possibility of targeting gene expression and inhibiting growth of intracellular mycobacteria by antisense oligonucleotide derivatives. Strong antisense activity and efficient uptake of the new RNA analogue, 2′-OMe PGO, by intracellular microorganisms revealed here may promote the development of novel therapeutic strategies to treat TB and prevent the emergence of drug-resistant mycobacterial strains.

Assessment of Antibiotic Levels, Multi-Drug Resistant Bacteria and Genetic Biomarkers in the Waters of the Rio Grande River Between the United States-Mexico Border

BACKGROUND

The worldwide emergence of multi-drug resistant bacteria has become a health crisis, as fewer or sometimes no antimicrobial agents are effective against these bacteria. The Rio Grande River is the natural boundary between the United States (US) and Mexico. It spans a border region between Texas, New Mexico and Mexico. Underserved populations on the Mexican side use the river for recreational purposes, while on the US side, the river is used for irrigation and as a source of drinking water.

OBJECTIVES

The purpose of the present study was to evaluate the concentration of antibiotic residues, to determine the presence of genetic elements conferring antibiotic resistance and to characterize multi-drug resistant bacteria in the waters of the Rio Grande River.

METHODS

Water samples were obtained from the Rio Grande River. Deoxyribonucleic acid (DNA) was extracted from both isolated bacteria and directly from the water. Amplification of selected genetic elements was accomplished by polymerase chain reaction. Identification and isolation of bacteria was performed through MicroScan autoSCAN-4. Fecal contamination was assessed by IDEXX Colilert. Antibiotic residues were determined by liquid chromatography and mass spectrometry.

RESULTS

Antibiotics were found in 92% of both water and sediment samples. Antibiotic concentrations ranged from 0.38 ng/L - 742.73 ng/L and 0.39 ng/l - 66.3 ng/g dry weight in water and sediment samples, respectively. Genetic elements conferring resistance were recovered from all collection sites. Of the isolated bacteria, 91 (64.08%) were resistant to at least two synergistic antibiotic combinations and 11 (14.79%) were found to be resistant to 20 or more individual antibiotics. Fecal contamination was higher during the months of April and July.

CONCLUSIONS

The 26 km segment of the Rio Grande River from Sunland Park NM to El Paso, TX and Juarez, Mexico is an area of concern due to poor water quality. The presence of multidrug resistant bacteria, antibiotics and mobile genetic elements may be a health hazard for the surrounding populations of this binational border region. Policies need to be developed for the appropriate management of the environmental natural resources in this border region.

COMPETING INTERESTS

The authors declare no competing financial interests.

Sanjin tablets for acute uncomplicated lower urinary tract infection (syndrome of dampness-heat in the lower jiao): protocol for randomized, double-blind, double-dummy, parallel control of positive drug, multicenter clinical trial

BACKGROUND

Acute uncomplicated lower urinary tract infection (UTI) is one of the most common bacterial infections. Patients usually present with dysuria, urinary urgency, urinary frequency, and suprapubic pain or tenderness. Approximately 150 million people are diagnosed with UTI each year worldwide. The high recurrence rate of lower UTI is a common problem of clinical treatment. The misuse of antibiotics has led to the emergence of a number of resistant bacterial strains. Thus, traditional Chinese medicine is considered as an alternative option for treating acute uncomplicated lower UTI. Thus, this study aims to evaluate the efficacy and safety of Sanjin tablets (SJT) for the treatment of acute uncomplicated lower UTI, explore whether SJT can reduce or substitute the use of antibiotics, and reduce the recurrence rate in the treatment of acute uncomplicated lower UTI.

METHODS/DESIGN

In this study, a randomized, double-blind, double-dummy, parallel control of positive drug, multicenter clinical study will be established. A total of 252 patients with acute uncomplicated lower UTI (syndrome of dampness-heat in the lower jiao) will be randomly allocated in the ratio of 1:1:1 to three groups: experimental group; control group 1; and control group 2. The experimental group receives Sanjin tablets plus levofloxacin tablets (LT) placebo; the control group 1 receives LT plus SJT placebo; and the control group 2 receives SJT plus LT on the first five days, SJT plus LT placebo on the last two days. Each group will be treated for seven days and followed-up 1-2 times. The primary outcome measures of effective rate and recurrence rate are symptoms. Secondary outcome measures of effective rate and recurrence rate are the urine leukocytes, bacteriology examination, and safety assessment. Outcomes will be assessed at baseline and after treatment.

DISCUSSION

This study protocol will provide the research data of efficacy and safety of SJT for the treatment of acute uncomplicated lower UTI. The first aim is to determine whether Sanjin tablets can reduce the use of antibiotics; the second aim is to determine whether Sanjin tablets can substitute the use of antibiotics. The recurrence rate will be assessed after cured to determine whether SJT can reduce the recurrence rate. The results of this study will improve the rational use of drugs, especially the rational application of antibiotics. It will also enable safety evaluation from laboratory indices and adverse events, which will provide reliable evidence for clinical treatment.

TRIAL REGISTRATION

ClinicalTrials.gov, NCT03658291 . Registered on 4 September 2018.

Clinical Trial Registration and Reporting: Drug Therapy and Prevention of Cardiac-Related Infections

Objective: Clinical trials are the source of evidence. ClinicalTrials.gov is valuable for analyzing current conditions. Until now, the state of drug interventions for heart infections is unknown. The purpose of this study was to comprehensively assess the characteristics of trials on cardiac-related infections and the status of drug interventions.

Methods: The website ClinicalTrials.gov was used to obtain all registered clinical trials on drug interventions for cardiac-related infections as of February 16, 2019. All registration studies were collected, regardless of their recruitment status, research results, and research type. Registration information, results, and weblink-publications of those trials were analyzed.

Results: A total of 45 eligible trials were evaluated and 86.7% of them began from or after 2008 while 91.1% of them adopted interventional study design. Of all trials, 35.6% were completed and 15.6% terminated. Besides, 62.2% of interventional clinical trials recruited more than 100 subjects. Meanwhile, 86.7% of the eligible trials included adult subjects only. Of intervention trials, 65.8% were in the third or fourth phase; 78.1% adopted randomized parallel assignment, containing two groups; 53.6% were masking, and 61.0% described treatment. Moreover, 41.5% of the trials were conducted in North America while 29.3% in Europe. Sponsors for 40.0% of the studies were from the industry. Furthermore, 48.9% of the trials mentioned information on monitoring committees, 24.4% have been published online, and 13.3% have uploaded their results. Drugs for treatments mainly contained antibiotics, among which glycopeptides, β-lactams, and lipopeptides were the most commonly studied ones in experimental group, with the former ones more common. Additionally, 16.2% of the trials evaluated new antimicrobials.

Conclusions: Most clinical trials on cardiac-related infections registered at ClinicalTrials.gov were interventional randomized controlled trials (RCTs) for treatment. Most drugs focused in trials were old antibiotics, and few trials reported valid results. It is necessary to strengthen supervision over improvements in results, and to combine antibacterial activity with drug delivery regimens to achieve optimal clinical outcomes.

Automated DNA hybridization transfer with movable super-paramagnetic microbeads in a microflow reactor

An automated DNA hybridization transfer in a microflow reactor is demonstrated by moving paramagnetic beads between two spatially separate solutions with different pH values. The microbeads-based microfluidic platform is fully automated and programmable. It employs a robust chemical procedure for specific DNA hybridization transfer in microfluidic devices under isothermal conditions based on reversible pH alterations. The method takes advantage of high-speed DNA hybridization and denaturation on beads under flow conditions, high fidelity of DNA hybridization, and small sample volumes. The microfluidic platform presented is saleable and applicable to many areas of modern biotechnology such as DNA hybridization chip microarrays, molecular computation, on-chip selection of functional nucleic acids, high-throughput screening of chemical libraries for drug discovery, and DNA amplification and sequencing.

Riboswitch distribution, structure, and function in bacteria

Riboswitches are gene control elements that directly bind to specific ligands to regulate gene expression without the need for proteins. They are found in all three domains of life, including Bacteria, Archaea, and Eukaryota. Riboswitches are mostly spread in bacteria and archaea. In this paper, we discuss the general distribution, structure, and function of 28 different riboswitch classes as we focus our attention on riboswitches in bacteria. Bacterial riboswitches regulate gene expression by four distinct mechanisms. They regulate the expression of a limited number of genes. However, most of these genes are responsible for the synthesis of essential metabolites without which the cell cannot function. Therefore, riboswitch distribution is also important for antibacterial drug development.

Cationic biaryl 1,2,3-triazolyl peptidomimetic amphiphiles: synthesis, antibacterial evaluation and preliminary mechanism of action studies

Synthetic small molecular antimicrobial peptidomimetics represent a promising new class of potential antibiotics due to their membrane-disrupting ability and their decreased propensity for bacterial resistance. A library of 43 mono- and di-cationic biaryl 1,2,3-triazolyl peptidomimetics was designed and synthesized based upon previously established lead biarylpeptidomimetics and a known pharmacophore. A reliable, facile and modular synthetic pathway allowed for the efficient synthesis of multiple unique scaffolds which were subjected to divergent derivatization to furnish the amphiphilic compounds. In vitro testing revealed enhanced antibacterial efficacy against a range of pathogenic bacteria, including bacterial isolates with methicillin, vancomycin, daptomycin, or multi-drug resistance. Preliminary time-kill kinetics and membrane-disruption assays revealed a likely membrane-active mechanism for the tested peptidomimetics. An optimal balance between hydrophobicity and cationic charge was found to be essential for reduced cytotoxicity/haemolysis (i.e. membrane selectivity) and enhanced Gram-negative activity. The cationic biaryl amphiphile 81 was identified as a potent, broad-spectrum peptidomimetic with activity against Gram-positive (methicillin-resistant Staphylococcus aureus - MIC = 2 μg/mL) and Gram-negative (Escherichia coli - MIC = 4 μg/mL) pathogenic bacteria.

Synergistic treatment strategies to combat resistant bacterial infections using Schiff base modified nanoparticulate - hydrogel system

Antibiotic resistance is of much prevalence and is one of the alarming realities for the rise in morbidity and mortality. Antibiotics; once regarded as wonder drugs have lost its credit of combating bacteria due to the rapid rise in variety of nosocomial pathogens. The underlying cause for the resistance spread is due to sudden drift in genetic mutation and the recalcitrant behavior of bacterial species. On the other hand, illegal and overconsumption of drugs fuels up the issue, wherein resistance development is directly proportional to the rate of drug consumption. Our pursuit was in reviving antibiotic, and further repurposing them into more potent formulation with reduced side effects to completely deplete resistant bacteria. In this work we present gentamicin encapsulated zein nanoparticle modified with Schiff base incorporated in immobilized chitosan-polyvinyl alcohol gel matrix([GM-ZNP]PG CsPVA) resulting in synergistic antibacterial activity. Schiff base modified zein nanoparticle exhibited an average diameter of 240 ± 8 nm and stability of -29.85 ± 2 mV. The nanocomposite system exhibited enhanced penetration rate when applied to dermis eliciting combinatorial antibacterial activity. Gentamicin in combination with Schiff base was found to lyse bacteria by ruining its cell integrity as depicted by SEM analysis. The formulation upon application stays intact to the impaired dermal tissues and releases drug in a sustained manner without the need of recurrent administration. The gel system was extremely biocompatible towards L929 cells without any toxicity. Overall, the work reports use of [GM-ZNP]PG CsPVA for resistant bacterial infections.

Discovery of an Antibacterial Isoindolinone-Containing Tetracyclic Polyketide by Cryptic Gene Activation and Characterization of Its Biosynthetic Gene Cluster

The major setback in natural product screening is the decreasing hit rate of novel bioactive compounds containing new chemical skeletons. Here we report the identification and biosynthesis of isoindolinomycin (Idm), an unprecedented bioactive polyketide with a novel isoindolinone-containing tetracyclic skeleton. Idm was discovered through the screening of rifampicin-resistant ( rif) mutants that were generated from nine actinomycete strains used in this study. Of the 114 rif mutants isolated, the mutant S55-50-5 was found to overproduce Idm, which is almost undetectable in the wild-type Streptomyces sp. SoC090715LN-16. An in silico analysis coupled with gene deletion experiments revealed a biosynthetic idmB gene cluster that is responsible for the production of Idm. The biosynthetic studies of Idm primarily focused on the formation of the five-membered ring in the tetracyclic structure and the attachment of the methyl group to the core structure. In addition, a malachite green phosphate assay performed using a stand-alone adenylation domain ( idmB21) demonstrated the involvement of glycine in the formation of the isoindolinone-containing skeleton. This study contributes to an increase in the structural diversity of polyketides and paves the way toward an understanding of the complete biosynthetic pathway of a novel class of tetracyclic polyketides.

Advances in the delivery of antisense oligonucleotides for combating bacterial infectious diseases

Discovery and development of new antibacterial drugs against multidrug resistant bacterial strains have become more and more urgent. Antisense oligonucleotides (ASOs) show immense potential to control the spread of resistant microbes due to its high specificity of action, little risk to human gene expression, and easy design and synthesis to target any possible gene. However, efficient delivery of ASOs to their action sites with enough concentration remains a major obstacle, which greatly hampers their clinical application. In this study, we reviewed current progress on delivery strategies of ASOs into bacteria, focused on various non-virus gene vectors, including cell penetrating peptides, lipid nanoparticles, bolaamphiphile-based nanoparticles, DNA nanostructures and Vitamin B12. The current review provided comprehensive understanding and novel perspective for the future application of ASOs in combating bacterial infections.

Effective drug combination for Caenorhabditis elegans nematodes discovered by output-driven feedback system control technique

Infections from parasitic nematodes (or roundworms) contribute to a significant disease burden and productivity losses for humans and livestock. The limited number of anthelmintics (or antinematode drugs) available today to treat these infections are rapidly losing their efficacy as multidrug resistance in parasites becomes a global health challenge. We propose an engineering approach to discover an anthelmintic drug combination that is more potent at killing wild-type Caenorhabditis elegans worms than four individual drugs. In the experiment, freely swimming single worms are enclosed in microfluidic drug environments to assess the centroid velocity and track curvature of worm movements. After analyzing the behavioral data in every iteration, the feedback system control (FSC) scheme is used to predict new drug combinations to test. Through a differential evolutionary search, the winning drug combination is reached that produces minimal centroid velocity and high track curvature, while requiring each drug in less than their EC₅₀ concentrations. The FSC approach is model-less and does not need any information on the drug pharmacology, signaling pathways, or animal biology. Toward combating multidrug resistance, the method presented here is applicable to the discovery of new potent combinations of available anthelmintics on C. elegans, parasitic nematodes, and other small model organisms.

The advancement of multidimensional QSAR for novel drug discovery - where are we headed?

INTRODUCTION

The Multidimensional quantitative structure-activity relationship (multidimensional-QSAR) method is one of the most popular computational methods employed to predict interesting biochemical properties of existing or hypothetical molecules. With continuous progress, the QSAR method has made remarkable success in various fields, such as medicinal chemistry, material science and predictive toxicology. Areas covered: In this review, the authors cover the basic elements of multidimensional -QSAR including model construction, validation and application. It includes and emphasizes the very recent developments of multidimensional -QSAR such as: HQSAR, G-QSAR, MIA-QSAR, multi-target QSAR. The advantages and disadvantages of each method are also discussed and typical examples of their application are detailed. Expert opinion: Although there are defects in multidimensional-QSAR modeling, it is still of enormous help to chemists, biologists and other researchers in various fields. In the authors' opinion, the latest more precise and feasible QSAR models should be further developed by integrating new descriptors, algorithms and other relevant computational techniques. Apart from being applied in traditional fields (e.g. lead optimization and predictive risk assessment), QSAR should be used more widely as a routine method in other emerging research fields including the modeling of nanoparticles(NPs), mixture toxicity and peptides.

Novel Bacterial Topoisomerase Inhibitors with Potent Broad-Spectrum Activity against Drug-Resistant Bacteria

The novel bacterial topoisomerase inhibitor class is an investigational type of antibacterial inhibitor of DNA gyrase and topoisomerase IV that does not have cross-resistance with the quinolones. Here, we report the evaluation of the in vitro properties of a new series of this type of small molecule. Exemplar compounds selectively and potently inhibited the catalytic activities of Escherichia coli DNA gyrase and topoisomerase IV but did not block the DNA breakage-reunion step. Compounds showed broad-spectrum inhibitory activity against a wide range of Gram-positive and Gram-negative pathogens, including biodefence microorganisms and Mycobacterium tuberculosis No cross-resistance with fluoroquinolone-resistant Staphylococcus aureus and E. coli isolates was observed. Measured MIC₉₀ values were 4 and 8 μg/ml against a panel of contemporary multidrug-resistant isolates of Acinetobacter baumannii and E. coli, respectively. In addition, representative compounds exhibited greater antibacterial potency than the quinolones against obligate anaerobic species. Spontaneous mutation rates were low, with frequencies of resistance typically <10^-8 against E. coli and A. baumannii at concentrations equivalent to 4-fold the MIC. Compound-resistant E. coli mutants that were isolated following serial passage were characterized by whole-genome sequencing and carried a single Arg38Leu amino acid substitution in the GyrA subunit of DNA gyrase. Preliminary in vitro safety data indicate that the series shows a promising therapeutic index and potential for low human ether-a-go-go-related gene (hERG) inhibition (50% inhibitory concentration [IC₅₀], >100 μM). In summary, the compounds' distinct mechanism of action relative to the fluoroquinolones, whole-cell potency, low potential for resistance development, and favorable in vitro safety profile warrant their continued investigation as potential broad-spectrum antibacterial agents.

Antimicrobial Nanoplexes meet Model Bacterial Membranes: the key role of Cardiolipin

Antimicrobial resistance to traditional antibiotics is a crucial challenge of medical research. Oligonucleotide therapeutics, such as antisense or Transcription Factor Decoys (TFDs), have the potential to circumvent current resistance mechanisms by acting on novel targets. However, their full translation into clinical application requires efficient delivery strategies and fundamental comprehension of their interaction with target bacterial cells. To address these points, we employed a novel cationic bolaamphiphile that binds TFDs with high affinity to form self-assembled complexes (nanoplexes). Confocal microscopy revealed that nanoplexes efficiently transfect bacterial cells, consistently with biological efficacy on animal models. To understand the factors affecting the delivery process, liposomes with varying compositions, taken as model synthetic bilayers, were challenged with nanoplexes and investigated with Scattering and Fluorescence techniques. Thanks to the combination of results on bacteria and synthetic membrane models we demonstrate for the first time that the prokaryotic-enriched anionic lipid Cardiolipin (CL) plays a key-role in the TFDs delivery to bacteria. Moreover, we can hypothesize an overall TFD delivery mechanism, where bacterial membrane reorganization with permeability increase and release of the TFD from the nanoplexes are the main factors. These results will be of great benefit to boost the development of oligonucleotides-based antimicrobials of superior efficacy.

Recent Developments in Antimicrobial Polymers: A Review

Antimicrobial polymers represent a very promising class of therapeutics with unique characteristics for fighting microbial infections. As the classic antibiotics exhibit an increasingly low capacity to effectively act on microorganisms, new solutions must be developed. The importance of this class of materials emerged from the uncontrolled use of antibiotics, which led to the advent of multidrug-resistant microbes, being nowadays one of the most serious public health problems. This review presents a critical discussion of the latest developments involving the use of different classes of antimicrobial polymers. The synthesis pathways used to afford macromolecules with antimicrobial properties, as well as the relationship between the structure and performance of these materials are discussed.

Resisting resistance: is there a solution for malaria?

INTRODUCTION

Currently, widely used antimalarial drugs have a limited clinical lifespan due to parasite resistance development. With resistance continuously rising, antimalarial drug discovery requires strategies to decrease the time of delivering a new antimalarial drug while simultaneously increasing the drug's therapeutic lifespan. Lessons learnt from various chemotherapeutic resistance studies in the fields of antibiotic and cancer research offer potentially useful strategies that can be applied to antimalarial drug discovery.

AREAS COVERED

In this review the authors discuss current strategies to circumvent resistance in malaria and alternatives that could be employed.

EXPERT OPINION

Scientists have been 'beating back' the malaria parasite with novel drugs for the past 49 years but the constant rise in antimalarial drug resistance is forcing the drug discovery community to explore alternative strategies. Avant-garde anti-resistance strategies from alternative fields may assist our endeavors to manage, control and prevent antimalarial drug resistance to progress beyond beating the resistant parasite back, to stopping it dead in its tracks.

Synthesis and antimicrobial activity of binaphthyl-based, functionalized oxazole and thiazole peptidomimetics

Thirty two new binaphthyl-based, functionalized oxazole and thiazole peptidomimetics and over thirty five novel leucine-containing intermediate oxazoles and thiazoles were prepared in this study. This includes the first examples of the direct C-5 arylation of an amino acid dipeptide-derived oxazole. Moderate to excellent antibacterial activity was observed for all new compounds across Gram positive isolates with MICs ranging from 1-16 μg mL(-1). Results for Gram negative E. coli and A. baumannii were more variable, but MICs as low as 4 μg mL(-1) were returned for two examples. Significantly, the in vitro results with a fluoromethyl-oxazole derivative collectively represent the best obtained to date for a member of our binaphthyl peptide antimicrobials.