New Generation Of Antibiotics Research Articles

New-generation biofilm effective antimicrobial peptides and a real-time anti-biofilm activity assay: CoMIC

Nowadays, it is very important to produce new-generation drugs with antimicrobial properties that will target biofilm-induced infections. The first target for combating these microorganisms, which are the source itself. Antimicrobial peptides, which are more effective than antibiotics due to their ability to kill microorganisms and use a different metabolic pathway, are among the new options today. The aim of this study is to develop new-generation antibiotics that inhibit both biofilm-producing bacteria and the biofilm itself. For this purpose, we designed four different peptides by combining two amino acid forms (D- and L-) with the same sequence having alpha helix structures. It was found that the combined use of these two forms can increase antimicrobial efficacy more than 30-fold. These results are supported by molecular modeling and scanning electron microscopy (SEM), at the same time cytotoxicity (IC50) and hemotoxicity (HC50) values remained within the safe range. Furthermore, antibiofilm activities of these peptides were investigated. Since the existing biofilm inhibition methods in the literature do not technically simulate the exact situation, in this study, we have developed a real-time observable biofilm model and a new detection method based on it, which we call the CoMIC method. Findings have shown that the NET1 peptide with D-leucine amino acid in its structure and the NET3 peptide with D-arginine amino acid in its structure are effective in inhibiting biofilm. As a conclusion, our peptides can be considered as potential next-generation broad-spectrum antibiotic molecule/drug candidates that might be used in biofilm and clinical important bacteria.Key points• Antimicrobial peptides were developed to inhibit both biofilms producing bacteria and the biofilm itself.• CoMIC will fill a very crucial gap in understanding biofilms and conducting the necessary quantitative studies.• Molecular modelling studies, NET1 peptide molecules tends to move towards and adhere to the membrane within nanoseconds.

Biosynthesis Optimization of Antibacterial-Magnetic Iron Oxide Nanoparticles from Bacillus megaterium.

The occurrence of antibiotic resistance on common bacterial agents and the need to use new generations of antibiotics have led to the use of various strategies for production. Taking inspiration from nature, using bio-imitation patterns, in addition to the low cost of production, is advantageous and highly accurate. In this research, we were able to control the temperature, shake, and synthesis time of the synthesis conditions of Bacillus megaterium bacteria as a model for the synthesis of magnetic iron nanoparticles and optimize the ratio of reducing salt to bacterial regenerating agents as well as the concentration of salt to create iron oxide nanoparticles with more favorable properties and produced with more antibacterial properties. Bacterial growth was investigated by changing the incubation times of pre-culture and overnight culture in the range of the logarithmic phase. The synthesis time, salt ratio, and concentration were optimized to achieve the size, charge, colloidal stability, and magnetic and antibacterial properties of nanoparticles. The amount of the effective substance produced by the bacteria was selected by measuring the amount of the active substance synthesized using the free radical reduction (DPPH) method. With the help of DPPH, the duration of the synthesis was determined to be one week. Characterizations such as UV-vis spectroscopy, FTIR, FESEM, X-ray, and scattering optical dynamics were performed and showed that the nanoparticles synthesized with a salt concentration of 80mM and a bacterial suspension to salt ratio of 2:1 are smaller in size and have a light scattering index, a PDI index close to 0.1, and a greater amount of reducing salt used in the reaction during one week compared to other samples. Moreover, they had more antibacterial properties than the concentration of 100mM. As a result, better characteristics and more antibacterial properties than common antibiotics were created on E. coli and Bacillus cereus.

Antimicrobial peptides as new-generation antibiotics against Mycobacterium

Abstract More than 10 million cases of tuberculosis (TB) in 2019 have made TB a global health problem. The increase in infection has caused an increase in the use of antibiotics for treatment, but with the spread of antibiotic use and the emergence of antibiotic resistance, the treatment has become difficult. This issue highlights the need to find a suitable alternative more than in the past. This matter emphasizes the urgency of discovering a viable substitute more than ever before. These obstacles underscore the necessity of developing innovative approaches that are not only cost-effective and efficient but also possess reduced levels of toxicity. Antimicrobial peptides (AMPs) possess a wide range of characteristics, which positions them as highly promising alternatives for a future era that follows the use of antibiotics. Here, we will focus on investigating AMPs from different sources, such as animal, nonanimal, and synthetic, with their inhibitory activity against TB as a therapeutic strategy. The aim of this study was to investigate different aspects of using AMPs to deal with Mycobacterium tuberculosis as a new strategy in its treatment. For this purpose, we studied more than 50 articles with the keywords peptide, AMP, and M. tuberculosis and investigated the importance of AMP against TB by searching valuable data sources such as PubMed, Scopus, Google Scholar, and Web of Science. In this study, the effect of antimicrobial peptides (AMPs) against mycobacteria was investigated. With the review done and considering all the advantages and challenges of AMPs, we concluded that this class of new antibiotics can be used as a long-term strategy to fight TB. As a result, we suggest research priorities to discover and optimize the challenges of these peptides as TB treatment and diagnostic methods in different countries.

Exploring the Antibacterial Potential of Semisynthetic Phytocannabinoid: Tetrahydrocannabidiol (THCBD) as a Potential Antibacterial Agent against Sensitive and Resistant Strains of Staphylococcus aureus.

Antimicrobial resistance (AMR) is one of the most challenging problems and is responsible for millions of deaths every year. We therefore urgently require new chemical entities with novel mechanisms of action. Phytocannabinoids have been adequately reported for the antimicrobial effect but not seriously pursued because of either stringent regulatory issues or poor drug-like properties. In this regard, the current work demonstrated the antibacterial potential of tetrahydrocannabidiol (THCBD, 4), a semisynthetic phytocannabinoid, against Staphylococcus aureus, the second-most widespread bug recognized by the WHO. THCBD (4) was generated from cannabidiol and subjected to extensive antibacterial screening. In in vitro studies, THCBD (4) demonstrated a potent MIC of 0.25 μg/mL against Gram-positive bacteria, S. aureus ATCC-29213. It is interesting to note that THCBD (4) has demonstrated strong effectiveness against efflux pump-overexpressing (SA-1199B, SA-K2191, SA-K2192, and Mupr-1) and multidrug-resistant (MRSA-15187) S. aureus strains. THCBD (4) has also shown a good effect in kill kinetic assays against ATCC-29213 and MRSA-15187. In the checkerboard assay, THCBD (4) has shown additive/indifference effects with several well-known clinically used antibiotics, tetracycline, mupirocin, penicillin G, and ciprofloxacin. THCBD (4) also exhibited good permeability in the artificial skin model. Most importantly, THCBD (4) has significantly reduced CFU in mice's in vivo skin infection models and also demonstrated decent plasma exposure with 16-17% oral bioavailability. Acute dermal toxicity of THCBD (4) suggests no marked treatment-related impact on gross pathophysiology. This attractive in vitro and in vivo profile of plant-based compounds opens a new direction for new-generation antibiotics and warrants further detailed investigation.

Micro-nanoemulsion and nanoparticle-assisted drug delivery against drug-resistant tuberculosis: recent developments.

SUMMARYTuberculosis (TB) is a major global health problem and the second most prevalent infectious killer after COVID-19. It is caused by Mycobacterium tuberculosis (Mtb) and has become increasingly challenging to treat due to drug resistance. The World Health Organization declared TB a global health emergency in 1993. Drug resistance in TB is driven by mutations in the bacterial genome that can be influenced by prolonged drug exposure and poor patient adherence. The development of drug-resistant forms of TB, such as multidrug resistant, extensively drug resistant, and totally drug resistant, poses significant therapeutic challenges. Researchers are exploring new drugs and novel drug delivery systems, such as nanotechnology-based therapies, to combat drug resistance. Nanodrug delivery offers targeted and precise drug delivery, improves treatment efficacy, and reduces adverse effects. Along with nanoscale drug delivery, a new generation of antibiotics with potent therapeutic efficacy, drug repurposing, and new treatment regimens (combinations) that can tackle the problem of drug resistance in a shorter duration could be promising therapies in clinical settings. However, the clinical translation of nanomedicines faces challenges such as safety, large-scale production, regulatory frameworks, and intellectual property issues. In this review, we present the current status, most recent findings, challenges, and limiting barriers to the use of emulsions and nanoparticles against drug-resistant TB.

Bactericidal activity of newly synthesized antimicrobial peptides against methicillin-resistant staphylococcus aureus and biofilm-forming methicillin-resistant staphylococcus aureus

Background: The emergence of multidrug-resistant bacteria (MDRB) poses a significant global challenge for healthcare professionals. Methicillin-resistant Staphylococcus aureus (MRSA), a prominent pathogen responsible for both hospital-acquired (nosocomial) and community-acquired infections, is particularly difficult to treat. Existing treatment options, such as vancomycin, linezolid, or clindamycin, have limitations. Therefore, there is a need for innovative approaches to combat infections caused by drug-resistant organisms. Methods: In this study, we synthesized a novel ultra-short antimicrobial peptide composed of three units of tryptophan and three units of lysine. We evaluated the effectiveness of this peptide against MRSA and MRSA that forms biofilms. Results: Encouraging results demonstrated that the peptide effectively killed both MRSA and biofilm-forming MRSA, while exhibiting low toxicity to human red blood cells. Additionally, our novel peptide showed excellent synergistic effects when combined with vancomycin against MRSA. Furthermore, when combined with levofloxacin and clarithromycin, our peptide exhibited synergistic effects against biofilm-forming MRSA. Conclusions: In conclusion, this study presents a novel ultra-short antimicrobial peptide (USAMP) that holds potential as a new generation of antibiotics to combat globally prevalent drug-resistant bacteria.

A Bioinspired Atomically Thin Nanodot Supported Single-Atom Nanozyme for Antibacterial Textile Coating.

Surface antibacterial coatings with outstanding antibacterial efficiency have attracted increasing attention in medical protective clothing and cotton surgical clothing. Although nanozymes, as a new generation of antibiotics, are used to combat bacteria, their catalytic performance remains far from satisfactory as alternatives to natural enzymes. Single-atom nanodots provide a solution to the low catalytic activity bottleneck of nanozymes. Here, atomically thin C3 N4 nanodots supported single Cu atom nanozymes (Cu-CNNDs) are developed by a self-tailoring approach, which exhibits catalytic efficiency of 8.09 × 105 M-1 s-1 , similar to that of natural enzyme. Experimental and theoretical calculations show that excellent peroxidase-like activity stems from the size effect of carrier optimizing the coordination structure, leading to full exposure of Cu-N3 active site, which improves the ability of H2 O2 to generate hydroxyl radicals (•OH). Notably, Cu-CNNDs exhibit over 99% superior antibacterial efficacy and are successfully grafted onto cotton fabrics. Thus, Cu-CNNDs blaze an avenue for exquisite biomimetic nanozyme design and have great potential applications in antibacterial textiles.

Antimicrobial and Cytotoxic Activities of the Secondary Metabolites of Endophytic Fungi Isolated from the Medicinal Plant Hyssopus officinalis.

According to the World Health Organization, it is estimated that by 2050, drug-resistant infections could cause up to 10 million deaths annually. Therefore, finding a new generation of antibiotics is crucial. Natural compounds from endophytic fungi are considered a potential source of new-generation antibiotics. The antimicrobial and cytotoxic effects of ethyl acetate extracts of nine endophytic fungal isolates obtained from Hyssopus officinalis were investigated for bioassay-guided isolation of the natural compounds. An extract of isolate VII showed the highest antimicrobial activities against Gram-positive bacteria Bacillus subtilis and Staphylococcus aureus (30.12 ± 0.20 mm and 35.21 ± 0.20 mm) and Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa (30.41 ± 0.23 mm and 25.12 ± 0.25 mm) among the tested extracts of isolates. Molecular identification of isolate VII confirmed it as Chaetomium elatum based on sequencing of its ITS genes, and it was discovered that this was the first time C. elatum had been isolated from H. officinalis. This isolate was cultured at a large scale for the isolation and identification of the active compound. Penicillic acid was isolated for the first time from C. elatum and its chemical structure was established by NMR spectroscopy. The penicillic acid showed strong antibacterial activities against Bacillus subtilis and Staphylococcus aureus with 20.68 mm and 25.51 mm inhibition zones, respectively. In addition, MIC and MBC values and antibiofilm activities of penicillic acid were determined. It was found that penicillic acid reduced the level of biofilms in proportion to antibacterial activity.

Use of Plant Extracts, Bee-Derived Products, and Probiotic-Related Applications to Fight Multidrug-Resistant Pathogens in the Post-Antibiotic Era

The ‘post-antibiotic’ era is near according to the World Health Organization (WHO). It is well known, due to the work of the scientific community, that drugs (antibiotics, antifungals, and other antimicrobial agents) are continuously becoming less effective, and multidrug-resistant (MDR) pathogens are on the rise. This scenario raises concerns of an impending global infectious disease crisis, wherein a simple opportunistic infection could be deadly for humans. The war against MDR pathogens requires innovation and a multidisciplinary approach. The present study provides comprehensive coverage of relevant topics concerning new antimicrobial drugs; it suggests that a combination of different natural products (such as plant extracts, honey, propolis, prebiotics, probiotics, synbiotics, and postbiotics), together with drug therapy, could be used as an adjuvant in standard treatments, thus allowing drug sensitivity in MDR pathogens to be restored, host immunity to be enhanced, and clinical efficiency to be improved. Currently, new and relevant developments in genomics, transcriptomics, and proteomics are available for research, which could lead to the discovery of new antimicrobial drugs and a new generation of antibiotics and non-antibiotics. However, several areas concerning natural products and their combination with standard drugs remain unclear. In an effort to advance new therapies for humankind, these gaps in the literature need to be addressed.

Glycopeptide Antibiotics Impair Neutrophil Effector Functions

Introduction: Neutrophilic granulocytes represent the first line of defense against microorganisms. Granulocytes phagocytose microorganisms and specifically synthesize oxygen radicals against them, which eventually kills the invaders. Methods: Neutrophilic granulocytes were isolated from peripheral blood of healthy volunteer donors. Putative interference of new-generation antibiotics with neutrophil function was tested using a collection of granulocyte-stimulating agents and Amplex™ Red-based plate assay and flow cytometry-based respiratory burst assays. In addition, phagocytosis of E. coli, IL-8 production, bactericidal activity, and CD62L expression of granulocytes were evaluated. Results: Of note, we found that the two glycopeptide antibiotics dalbavancin and teicoplanin inhibited ROS production upon granulocyte activation via different signaling pathways in a dose-dependent manner. Dalbavancin also blocked the PMA-induced shedding of CD62L. In contrast, the oxazolidinone antibiotics tedizolid and linezolid had no effect on neutrophil function, while the combination of ceftazidime/avibactam dose dependently inhibited the fMLP/Cytochalasin B-induced granulocyte burst in a dose-dependent manner. Additionally, we showed that dalbavancin and teicoplanin as well as sulfametrole/trimethoprim and ceftazidime/avibactam inhibited baseline and PMA-induced IL-8 production by neutrophilic granulocytes. Moreover, dalbavancin impaired the bactericidal activity of neutrophilic granulocytes. Conclusion: We here identified hitherto unknown inhibitory effects of several classes of antibiotics on the effector functions of neutrophilic granulocytes.

The Occurrence of Methicillin-Resistant Staphylococcus Aureus (MRSA) Around the World and Antibiotic Therapy for Selected Infections Caused By MRSA

Abstract Staphylococcus aureus is a Gram-positive bacterium, which can cause serious bacterial infections in humans. It constitutes an important etiological factor of many diseases, for instance, soft tissue and skin infections (including skin boils and abscesses), as well as life-threatening necrotizing pneumonia or toxic shock syndrome. It is estimated that about 25–30% of people are carriers of S. aureus mainly in the anterior nostrils. A smaller percentage of people are carriers of methicillin-resistant S. aureus (MRSA). In accordance with its definition, methicillin-resistant S. aureus is resistant to almost all β-lactam antibiotics. This phenomenon is mainly caused by the presence of penicillin-binding protein in the cell wall – PBP2a, which is the product of the mecA gene, which is part of the complex called SCCmec (staphylococcal cassette chromosome mec). Methicillin-resistant S. aureus (MRSA) results in endemic in hospitals around the world and are one of the leading causes of morbidity and mortality in society. Infections initiated by hospital strains of MRSA (health care-associated MRSA, HA-MRSA) concern mainly immunocompromised patients after surgery. In addition, there are populations of acommunity-associated MRSA (CA-MRSA) strains and populations of livestock-associated MRSA (LA-MRSA) strains. The treatment of infections with MRSA etiology, after exhausting the possibilities of standard antibiotic therapy with the use of i.e. vancomycin, is based on treatment with new-generation antibiotics, such as dalbavacin.

Recombinant Antimicrobial Peptide OaBac5mini Alleviates Inflammation in Pullorum Disease Chicks by Modulating TLR4/MyD88/NF-κB Pathway.

Pullorum disease (PD), caused by Salmonella Pullorum (S. Pullorum), is a serious threat to the poultry industry worldwide. Antimicrobial peptides (AMPs) have drawn extensive attention as new-generation antibiotics because of their broad antimicrobial spectrum, low resistance, and low cytotoxicity. AMP OaBac5mini exhibits strong antibacterial activity against Gram-negative bacteria, but its efficacy and anti-inflammatory effects on chicks with PD remain unclear. The aim of this study was to generate recombinant OaBac5mini via the Escherichia coli (E. coli) recombinant expression system and evaluate its antibacterial effect against S. Pullorum in vitro and in vivo. Real-time cellular analysis (RTCA) results showed that recombinant OaBac5mini exhibited no cytotoxicity on IPEC-J2 and RAW 264.7 cells and significantly alleviated the drop in the cell index of S. Pullorum-infected cells (p < 0.0001). In the chick model of PD, recombinant OaBac5mini significantly attenuated the increase in organ indexes (heart, liver, spleen, and kidney) and bacterial loads (liver and spleen) induced by S. Pullorum. Histopathology examination showed that recombinant OaBac5mini ameliorated histopathological changes and inflammation in chicks with PD, including impaired epithelium of duodenal villi, infiltration of pseudoacidophilic granulocytes in the cecum and bursa of Fabricius, congested blood clots and increased macrophages in the liver, and increased lymphoid nodule and B lymphocytes in the spleen. Western blot and quantitative real-time PCR (qRT-PCR) results indicated that recombinant OaBac5mini alleviated inflammation by modulating innate immunity through the TLR4/MyD88/NF-κB pathway and by suppressing the expression of pro-inflammatory cytokines. These results suggested that recombinant OaBac5mini has good potential as a clinical substitute for antibiotics in PD intervention.

Targeting staphylococcal bone infections

A novel quinolone antibiotic was developed by Shiladitya Sengupta and colleagues using molecular-docking simulation, and one lead compound, VCD-077, was selected based on this strategy.1 Antimicrobial resistance is increasing, driven by widespread antibiotic overuse in medical and agricultural settings.2 Paradoxically, despite the urgent need to develop a new generation of antibiotics, their marketability is suppressed, partly because the new antibacterial drug may quickly develop new resistance and the development of new antibiotics is sluggish.3, 4 The ideal next-generation antibiotic should demonstrate excellent activity against drug-resistant bacteria, good biosafety, flexible drug delivery, and the ability to retard the development of resistance. In this regard, recently researchers have focused on developing novel antibiotics by improving drug performance, availability, targeted enrichment, and reducing systemic toxicity. Reporting in Nature Biomedical Engineering, Shiladitya Sengupta and colleagues now show that VCD-077 screened by molecular-docking simulations exhibits excellent activity against drug-resistant bacteria and its biofilms, reduces the development of bacterial resistance and is compatible with bone cement for local delivery and treatment of staphylococcal bone infections in rats (Figure 1).1 Bone infections are rising rapidly due to accidental fractures and the global aging population.5 Sengupta and co-authors designed a series of quinolone antibiotics using molecular-docking simulation. They selected VCD-077 from 17 candidate antibiotics, which can effectively against clinical drug-resistant staphylococcal and retard the development of resistance. The minimal inhibitory concentration (MIC) of ciprofloxacin, Staphylococcus aureus sensitive antibiotics, increased stepwise to 64.0 μg/ml by the 20th passage to S. aureus. While S. aureus were still sensitive to VCD-077 even at the 28th passage. Specifically, VCD-077 is potent against S. aureus and Staphylococcus epidermidis biofilms because it is a weak acid with a single pKa of 5.8, that is, it still maintains antibacterial activity at pH 5.5–7.4. In contrast, gentamicin lost part of its activity at acid pH 5.5. Therefore, VCD-077 has a unique advantage in the prevailing weakly acidic infected bone environment. Notably, VCD-077 is physicochemically compatible with polymethylmethacrylate bone cement, exhibits desired pharmacokinetics without loss of mechanical properties of bone cement. VCD-077-impregnated bone cement showed more powerful anti-infective activity compared with either FDA-approved rifampin or gentamicin-impregnated bone cement. Overall, the authors show that VCD-077-impregnated bone cement could be used as rational next-generation drugs or coatings to treat bone infections. The high efficacy of Sengupta and co-authors' VCD-077-impregnated bone cement suggests that flexible local administration can be achieved at ideal safe concentration, and is effective against resistant strains, as well as delaying the development of new resistance. However, before VCD-077-impregnated bone cement can be considered for the treatment of clinical bone infection, three main challenges were compelled to be discussed. First, the authors used rodents in this experiment, which may be differences between the efficacy of antibiotics-impregnated bone cement in rodents and human bones. Studies using larger animal infection models (such as pigs and monkeys) would employ to corroborate the impressive antimicrobial activity in rat models. Second, significant biosafety assessment under good laboratory practice guidelines should be performed. And third, new antibiotic development should focus on specific screening molecules and combinations with emerging nanoparticle-based delivery systems that can target both resistant and persistent bacterial populations.6 Developing novel antibacterial agent delivery systems to improve the bioavailability of antibiotics is a promising strategy for increasing the lifespan of newly developed antibiotics. Integration of such novel antibiotics and combinations into nanoparticle-based delivery systems or coating implants might transform the landscape of infectious diseases. Drafting the article: Zhang Xiangchun. Revising the manuscript: Xulin Hu and Hongping Chen. All authors have read and approved the final manuscript This research was supported by the National Key Research and Development Program of China (2021YFD1601102), Central Public-interest Scientific Institution Basal Research Fund (No. Y2022QC24), and Innovative Program of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2021-TRI, CAAS-ZDRW202011). The authors declare no conflict of interest. Not applicable. Not applicable.

2D-MoS2-supported copper peroxide nanodots with enhanced nanozyme activity: application in antibacterial activity

Peroxidase (POD)-like nanozymes are an upcoming class of new-generation antibiotics that are efficient for broad-spectrum antibacterial action.

Antimicrobial Activity and Immunomodulatory Properties of Acidocin A, the Pediocin-like Bacteriocin with the Non-Canonical Structure.

Pediocin-like bacteriocins are among the natural antimicrobial agents attracting attention as scaffolds for the development of a new generation of antibiotics. Acidocin A has significant structural differences from most other members of this subclass. We studied its antibacterial and cytotoxic activity, as well as effects on the permeability of E. coli membranes in comparison with avicin A, the typical pediocin-like bacteriocin. Acidocin A had a more marked tendency to form an alpha-helical structure upon contact with detergent micelles, as was shown by CD spectroscopy, and demonstrated considerably less specific mode of action: it inhibited growth of Gram-positive and Gram-negative strains, which were unsusceptible to avicin A, and disrupted the integrity of outer and inner membranes of E. coli. However, the peptide retained a low toxicity towards normal and tumor human cells. The effect of mutations in the pediocin box of acidocin A (on average, a 2-4-fold decrease in activity) was less pronounced than is usually observed for such peptides. Using multiplex analysis, we showed that acidocin A and avicin A modulated the expression level of a number of cytokines and growth factors in primary human monocytes. Acidocin A induced the production of a number of inflammatory mediators (IL-6, TNFα, MIG/CXCL9, MCP-1/CCL2, MCP-3/CCL7, and MIP-1β) and inhibited the production of some anti-inflammatory factors (IL-1RA, MDC/CCL22). We assumed that the activity of acidocin A and similar peptides produced by lactic acid bacteria might affect the functional state of the human intestinal tract, not only through direct inhibition of various groups of symbiotic and pathogenic bacteria, but also via immunomodulatory effects.

ABP-Finder: A Tool to Identify Antibacterial Peptides and the Gram-Staining Type of Targeted Bacteria.

Multi-drug resistance in bacteria is a major health problem worldwide. To overcome this issue, new approaches allowing for the identification and development of antibacterial agents are urgently needed. Peptides, due to their binding specificity and low expected side effects, are promising candidates for a new generation of antibiotics. For over two decades, a large diversity of antimicrobial peptides (AMPs) has been discovered and annotated in public databases. The AMP family encompasses nearly 20 biological functions, thus representing a potentially valuable resource for data mining analyses. Nonetheless, despite the availability of machine learning-based approaches focused on AMPs, these tools lack evidence of successful application for AMPs' discovery, and many are not designed to predict a specific function for putative AMPs, such as antibacterial activity. Consequently, among the apparent variety of data mining methods to screen peptide sequences for antibacterial activity, only few tools can deal with such task consistently, although with limited precision and generally no information about the possible targets. Here, we addressed this gap by introducing a tool specifically designed to identify antibacterial peptides (ABPs) with an estimation of which type of bacteria is susceptible to the action of these peptides, according to their response to the Gram-staining assay. Our tool is freely available via a web server named ABP-Finder. This new method ranks within the top state-of-the-art ABP predictors, particularly in terms of precision. Importantly, we showed the successful application of ABP-Finder for the screening of a large peptide library from the human urine peptidome and the identification of an antibacterial peptide.

Rational Design of RN15m4 Cathelin Domain-Based Peptides from Siamese Crocodile Cathelicidin Improves Antimicrobial Activity.

Antimicrobial peptides are becoming a new generation of antibiotics due to their therapeutic potential and ability to decrease drug-resistant bacteria development. Cathelicidins are known as effective peptides of vertebrate immunity that play crucial roles in the defensive strategy against pathogens. To improve its potency, the RN15 antibacterial peptide derived from the cathelin domain of Crocodylus siamensis cathelicidin has been modified and its antimicrobial properties investigated. Peptides were derived by template-based and physicochemical designation. The RN15 derivative peptides were predicted through their structure modeling, antimicrobial potency, and peptide-membrane calculation. The antimicrobial and cytotoxic activities of candidate peptides were investigated. Simultaneous consideration of physicochemical characteristics, secondary structure modeling, and the result of antimicrobial peptide tools prediction indicated that RN15m4 peptide was a candidate derivative antimicrobial peptide. The RN15m4 peptide expresses antimicrobial activity against most Gram-positive and Gram-negative bacteria and fungi with a lower minimum inhibition concentration (MIC) than the parent peptide. Besides, the time-killing assay shows that the designed peptide performed its ability to quickly kill bacteria better than the original peptide. Scanning electron microscopy (SEM) displayed the destruction of the bacterial cell membrane caused by the RN15m4 peptide. In addition, the RN15m4 peptide exhibits low hemolytic activity and low cytotoxic activity as good as the template peptide. The RN15m4 peptide performs a range of antimicrobial activities with low cell toxicity. Our study has illustrated the combination approach to peptide design for potent antibiotic peptide discovery.

An ultrasound activable metal-phenolic network nano-antibiotics for in vivo on-site infection therapy

Antibiotic is one of the greatest discoveries in human history. It has drastically promoted modern medicine and extended the average human lifespan. However, antibiotic resistance has become a global crisis today and the development of novel antibiotics is highly demanded. The traditional antibiotics not only kill the pathogen but also damage the resident microbiome in the human body, thus promoting antibiotic resistance and elevating the risk of patients for new infection. Here, we fabricated an activable metal-phenolic network nano-antibiotics (PEG-P18-Ag NPs) that can be selectively activated on the site of infection, thus presumably avoiding their impacts on the resident microbiome. We showed that PEG-P18-Ag NPs per se do not have any antibacterial activity. However, upon activation by the ultrasound, they triggered the generation of reactive oxygen species. Consequently, PEG-P18-Ag NPs remarkably killed various multi-drug resistant bacteria and established biofilms in vitro and in vivo. By RNA sequencing, we revealed that activated PEG-P18-Ag NPs produced a profound damaging effect on the bacteria. Collectively, we provided a novel approach for the new generation of antibiotics that selectively target infected bacteria.

Docking-Based Virtual Screening for the Discovery of 1,3,4-Oxadiazoles as Aminoacyl-tRNA Synthetase Inhibitors

Aminoacyl-tRNA synthetases (aaRSs) are one of the leading targets for the development of antibiotic agents. In this paper, we reported the discovery of aaRS inhibitors using a structure-based virtual screening method. The interactions of 52 designed structures with the methionyl-tRNA synthetase (MetRS) target were performed by docking the ligands into the active zone of the MetRS using Autodock Vina. The data revealed 14 compounds displaying interactions with key amino acids (Asp287, Tyr250, Val473, Trp474, Phe522, Ile519, Ala477, Leu478, and His523) at the binding pocket of the enzyme, indicating their potential as MetRS inhibitors. These results could be served as the references for further synthetic work and bioassays experiments for discovering MetRS inhibitors and other pharmaceutical agents that may assist in the generation of new antibiotics.

Nanoscale Features of Tunable Bacterial Outer Membrane Models Revealed by Correlative Microscopy.

The rise of antibiotic resistance is a growing worldwide human health issue, with major socioeconomic implications. An understanding of the interactions occurring at the bacterial membrane is crucial for the generation of new antibiotics. Supported lipid bilayers (SLBs) made from reconstituted lipid vesicles have been used to mimic these membranes, but their utility has been restricted by the simplistic nature of these systems. A breakthrough in the field has come with the use of outer membrane vesicles derived from Gram-negative bacteria to form SLBs, thus providing a more physiologically relevant system. These complex bilayer systems hold promise but have not yet been fully characterized in terms of their composition, ratio of natural to synthetic components, and membrane protein content. Here, we use correlative atomic force microscopy (AFM) with structured illumination microscopy (SIM) for the accurate mapping of complex lipid bilayers that consist of a synthetic fraction and a fraction of lipids derived from Escherichia coli outer membrane vesicles (OMVs). We exploit the high resolution and molecular specificity that SIM can offer to identify areas of interest in these bilayers and the enhanced resolution that AFM provides to create detailed topography maps of the bilayers. We are thus able to understand the way in which the two different lipid fractions (natural and synthetic) mix within the bilayers, and we can quantify the amount of bacterial membrane incorporated into the bilayer. We prove the system’s tunability by generating bilayers made using OMVs engineered to contain a green fluorescent protein (GFP) binding nanobody fused with the porin OmpA. We are able to directly visualize protein–protein interactions between GFP and the nanobody complex. Our work sets the foundation for accurately understanding the composition and properties of OMV-derived SLBs to generate a high-resolution platform for investigating bacterial membrane interactions for the development of next-generation antibiotics.