Antibiotics for emerging pathogens

Regional-scale investigation for microbial competition-through-environment interactions modulating antibiotic resistance

Originating from a long history of competition between microbes, antibiotic resistance is a serious global health concern. To avoid the risk of antibiotic resistance, tremendous efforts have been directed towards restricting antibiotic consumption worldwide, but to date with limited success. Resistance is governed by multiple pressures from natural and anthropogenic origins which further create problems with control. This study identifies a chain of links from antibiotic resistant genes (ARGs) to microbial communities to environmental pressures in the surface sediments of forty-two lake clusters across the 1000-km Yangtze Basin of China, and attempts to expound on a control pathway for this resistance risk. Results show that eleven of the 670 bacterial families can be classified as antibiotic-resistant or nonresistant communities which antagonize each other. In natural systems, antagonistic competition controls the increase and decrease in ARGs. Superiority of antibiotic-resistant strains initiates a loss in microbial diversity associated with the prevalence of resistance risk. This study shows that, antibiotics shape the evolution of ARGs in resistant communities through a nonlinear role of orientor; other selected pressures serve as a facilitator to enhance the antibiotic resistance through an investigated chain of links. Furthermore, according to tolerances of the classified communities, abiogenetic development through temperature, salinity and Mg were identified and selected for study from seventy lake parameters. Linear feedbacks to selected pressures make the nonresistant communities outcompete the resistant communities, theoretically modulating the risk of antibiotic resistance.

Scaffold Modifications in Erythromycin Macrolide Antibiotics. A Chemical Minireview

Clarithromycin and congeners are important antibacterial members of the erythromycin A 14-membered macrocyclic lactone family. The macrolide scaffold consists of a multifunctional core that carries both chemically reactive and non-reactive substituents and sites. Two main approaches are used in the preparation of the macrolides. In semisynthesis, the naturally occurring macrocycle serves as a substrate for structural modifications of peripheral substituents. This review is focused on substituents in non-activated positions. In the total synthesis approach, the macrolide antibiotics are constructed by a convergent assembly of building blocks from presynthesized substrates or substrates prepared by biogenetic engineering. The assembled block structures are linear chains that are cyclized by macrolactonization or by metal-promoted cross-coupling reactions to afford the 14-membered macrolactone. Pendant glycoside residues are introduced by stereoselective glycosylation with a donor complex. When available, a short summary of antibacterial MIC data is included in the presentations of the structural modifications discussed.

Novel Treatments against Mycobacterium tuberculosis Based on Drug Repurposing

Tuberculosis is the leading cause of death, worldwide, due to a bacterial pathogen. This respiratory disease is caused by the intracellular pathogen Mycobacterium tuberculosis and produces 1.5 million deaths every year. The incidence of tuberculosis has decreased during the last decade, but the emergence of MultiDrug-Resistant (MDR-TB) and Extensively Drug-Resistant (XDR-TB) strains of M. tuberculosis is generating a new health alarm. Therefore, the development of novel therapies based on repurposed drugs against MDR-TB and XDR-TB have recently gathered significant interest. Recent evidence, focused on the role of host molecular factors on M. tuberculosis intracellular survival, allowed the identification of new host-directed therapies. Interestingly, the mechanism of action of many of these therapies is linked to the activation of autophagy (e.g., nitazoxanide or imatinib) and other well-known molecular pathways such as apoptosis (e.g., cisplatin and calycopterin). Here, we review the latest developments on the identification of novel antimicrobials against tuberculosis (including avermectins, eltrombopag, or fluvastatin), new host-targeting therapies (e.g., corticoids, fosfamatinib or carfilzomib) and the host molecular factors required for a mycobacterial infection that could be promising targets for future drug development.

Combating Antibiotic-Resistant Gram-Negative Bacteria Strains with Tetracycline-Conjugated Carbon Nanoparticles

Nontoxic carbon nanoparticle samples prepared by both bottom-up and top-down approaches do not inhibit Gram-negative bacterial growth, indicating excellent biocompatibilities. However, cell growth inhibitory efficacies increase considerably when the carbon nanoparticles are conjugated with the antibiotic tetracycline. In tetracycline-resistant bacteria, these efficacies can approach tenfold higher activities when compared to tetracycline alone. No structural abnormality such as membrane disruptions is evident in the tested bacterial strains; this is in contrast with other nanocarbon systems such as graphene oxides, carbon nanotubes, and amine-functionalized carbon nanoparticles which do exhibit membrane disruptions. In comparison, the tetracycline-conjugated carbon nanoparticles induce membrane perturbations (but not membrane disruptions), inhibiting bacterial efflux mechanisms. It is proposed that when tetracycline is conjugated to the surface of carbon nanoparticles, it functions to direct the nanoparticles to membrane-associated tetracycline efflux pumps, thereby blocking and subsequently inhibiting their function. The conjugation between biocompatible carbon nanoparticles and subtherapeutic but well-established antibiotic molecules may provide hybrid antibiotic assembly strategies resulting in effective multidrug efflux inhibition for combating antibiotic resistance.

ent-Beyerane Diterpenes as a Key Platform for the Development of ArnT-Mediated Colistin Resistance Inhibitors

Colistin is a last-resort antibiotic for the treatment of multidrug resistant Gram-negative bacterial infections. Recently, a natural ent-beyerene diterpene was identified as a promising inhibitor of the enzyme responsible for colistin resistance mediated by lipid A aminoarabinosylation in Gram-negative bacteria, namely, ArnT (undecaprenyl phosphate-alpha-4-amino-4-deoxy-l-arabinose arabinosyl transferase). Here, semisynthetic analogues of hit were designed, synthetized, and tested against colistin-resistant Pseudomonas aeruginosa strains including clinical isolates to exploit the versatility of the diterpene scaffold. Microbiological assays coupled with molecular modeling indicated that for a more efficient colistin adjuvant activity, likely resulting from inhibition of the ArnT activity by the selected compounds and therefore from their interaction with the catalytic site of ArnT, an ent-beyerane scaffold is required along with an oxalate-like group at C-18/C-19 or a sugar residue at C-19 to resemble L-Ara4N. The ent-beyerane skeleton is identified for the first time as a privileged scaffold for further cost-effective development of valuable colistin resistance inhibitors.

Differential effects of the Akt pathway on the internalization of Klebsiella by lung epithelium and macrophages

Host response to lung infection includes coordinated efforts of multiple cell types, including the lung epithelium and macrophages. Importantly, both the lung epithelium and macrophages can internalize and clear invading pathogens. However, the mechanisms and their ability to internalize or phagocytose differ. Akt is a key cellular pathway that controls cell proliferation and survival, in addition to its role in host defense. The role of the Akt pathway was assessed using pharmacological Akt modulators in lung epithelial (A549) and macrophage (RAW 264.7) cell lines during Klebsiella bacterial infection. Our data show that the inhibition of the Akt pathway using specific Akt inhibitor MK2206 increased the phagocytic ability of lung epithelial cells but not of macrophages. In contrast, the activation of Akt using specific activator SC-79 decreased the phagocytic ability of epithelial cells, while it increased the phagocytic ability of macrophages. The altered phagocytic ability in both cell types using Akt modulators was not due to changes in bacterial adhesion to the host cell. The clinical usefulness of these Akt modulators may vary based on the type of infection and on the relative contribution of epithelial cells and macrophages in clearing the particular bacterial infection. The Akt pathway has differential roles in the internalization of Klebsiella bacteria by respiratory epithelial cells and immune cells.

Synthesis of Degraded Limonoid Analogs as New Antibacterial Scaffolds against Staphylococcus aureus

Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) have become serious infections in humans and ruminants. S. aureus strains are showing rapid changes to develop resistance in traditional antibiotic-containing systems. In the continuous fierce fight against the emergent multi-drug resistant bacterial strains, straightforward and scalable synthetic procedures to produce new active molecules are in demand. Analysis of molecular properties points to degraded limonoids as promising candidates. In this article, we report a simple synthetic approach to obtain degraded limonoid analogs as scaffolds for new antibacterial molecules. The minimum inhibitory concentrations against S. aureus were evaluated for the stereoisomer mixtures by the broth microdilution method. Analysis of results showed that the acetylated derivatives were the most active of them all.

Role of symbiosis in the discovery of novel antibiotics

Antibiotic resistance has been an ongoing challenge that has emerged almost immediately after the initial discovery of antibiotics and requires the development of innovative new antibiotics and antibiotic combinations that can effectively mitigate the development of resistance. More than 35,000 people die each year from antibiotic resistant infections in just the United States. This signifies the importance of identifying other alternatives to antibiotics for which resistance has developed. Virtually, all currently used antibiotics can trace their genesis to soil derived bacteria and fungi. The bacteria and fungi involved in symbiosis is an area that still remains widely unexplored for the discovery and development of new antibiotics. This brief review focuses on the challenges and opportunities in the application of symbiotic microbes and also provides an interesting platform that links natural product chemistry with evolutionary biology and ecology.

Cysteine Potentiates Bactericidal Antibiotics Activity Against Gram-Negative Bacterial Persisters

Purpose

Bacterial metabolism regulators offer a novel productive strategy in the eradication of antibiotic refractory bacteria, particularly bacterial persisters. However, the potential of amino acids in the fight against Gram-negative bacterial persisters has not been fully explored. The aim of this study is to investigate the potentiation of amino acids to antibiotics in combating Gram-negative bacterial persisters and to reveal the underlying mechanisms of action.

Methods

Bactericidal activity of antibiotics in the absence or presence of amino acids was evaluated through detecting the reduction of bacterial CFUs. The ratio of NAD⁺/NADH in E. coli B2 persisters was determined using assay kit with WST-8. Bacterial respiration and ROS production were measured by the reduction of iodonitrotetrazolium chloride and fluorescent probe 2′,7′-dichlorodihydrofluorescein diacetate, respectively.

Results

In this study, we found that cysteine possesses excellent synergistic bactericidal activity with ciprofloxacin against multiple Gram-negative bacterial persisters. Furthermore, the potentiation of cysteine was evaluated in exponential and stationary-phase E. coli ATCC 25922 and E. coli B2. Interestingly, cysteine significantly improves three bactericidal antibiotics killing against stationary-phase bacteria, but not exponential-phase bacteria, implying that the effect of cysteine correlates with the metabolic state of bacteria. Mechanistic studies revealed that cysteine accelerates the bacterial TCA cycle and promotes bacterial respiration and ROS production. These metabolic regulation effects of cysteine re-sensitive bacterial persisters to antibiotic killing.

Conclusion

Collectively, our study highlights the synergistic bactericidal activity of bacterial metabolism regulators such as cysteine with commonly used antibiotics against Gram-negative bacterial persisters.

Tideglusib and Its Analogues As Inhibitors of Staphylococcus aureus SrtA

Sortase A (SrtA) anchors surface proteins to the cell wall envelope, and it has attracted increasing interesting as a potential antivirulence target. Several small-molecule inhibitors for SrtA have been developed, but target validation remains largely underexplored. Herein, we report a new class of SrtA inhibitors that supports antivirulence therapy through small-molecule targeting of SrtA. Tideglusib (TD), a drug candidate for myotonic dystrophy, was outstanding in high-throughput screening. A concise synthetic route quickly provided TD analogues, and the structure-activity relationships for SrtA inhibition have been established from those analogues. Several compounds largely retained the in vitro potency and exhibited a better solubility than TD. Additionally, TD attenuated virulence-related phenotypes in vitro and protected mice against lethal S. aureus USA300 bacteremia. Our study indicates that TD and its analogues could be new candidates as SrtA inhibitors with potential in the development of new antivirulence agents.

PDA/Cu Bioactive Hydrogel with "Hot Ions Effect" for Inhibition of Drug-Resistant Bacteria and Enhancement of Infectious Skin Wound Healing

Quick and effective sterilization of drug-resistant bacteria inevitably became an ever-growing global challenge. In this study, a multifunctional composite (PDA/Cu-CS) hydrogel mainly composed of polydopamine (PDA) and copper-doped calcium silicate ceramic (Cu-CS) was prepared. It was confirmed that PDA/copper (PDA/Cu) complexing in the composite hydrogel played a key role in enhancing the photothermal performance and antibacterial activity. Through a unique "hot ions effect", created by the heating of Cu ions through the photothermal effect of the composite hydrogel, the hydrogel showed high-efficiency, quick, and long-term inhibition of methicillin-resistant Staphylococcus aureus and Escherichia coli. In addition, the hydrogel possessed remarkable bioactivity to stimulate angiogenesis. The in vivo results confirmed that the "hot ions effect" of the composite hydrogel removed existing infection in the wound area efficiently and significantly promoted angiogenesis and collagen deposition during infectious skin wound healing. Our results suggested that the design of multifunctional hydrogels with "hot ions effect" may be an effective therapeutic approach for the treatment of infectious wounds.

FtsZ-Independent Mechanism of Division Inhibition by the Small Molecule PC190723 in Escherichia coli

While cell division is a critical process in cellular proliferation, very few antibiotics have been identified that target the bacterial cell-division machinery. Recent studies have shown that the small molecule PC190723 inhibits cell division in several Gram-positive bacteria, with a hypothesized mechanism of action involving direct targeting of the tubulin homolog FtsZ, which is essential for division in virtually all bacterial species. Here, it is shown that PC190723 also inhibits cell division in the Gram-negative bacterium Escherichia coli if the outer membrane permeability barrier is compromised genetically or chemically. The results show that the equivalent FtsZ mutations conferring PC190723 resistance in Staphylococcus aureus do not protect E. coli against PC190723, and that suppressors of PC190723 sensitivity in E. coli, which do not generically decrease outer membrane permeability, do not map to FtsZ or other division proteins. These suppressors display a wide range of morphological and growth phenotypes, and one exhibits a death phenotype in the stationary phase similar to that of a mutant with disrupted lipid homeostasis. Finally, a complementing FtsZ-msfGFP fusion is used to show that PC190723 does not affect the Z-ring structure. Taken together, the findings suggest that PC190723 inhibits growth and division in E. coli without targeting FtsZ. This study highlights the importance of utilizing a combination of genetic, chemical, and single-cell approaches to dissect the mechanisms of action of new antibiotics, which are not necessarily conserved across bacterial species.

Possible drugs for the treatment of bacterial infections in the future: anti-virulence drugs

Antibiotic resistance is a global threat that should be urgently resolved. Finding a new antibiotic is one way, whereas the repression of the dissemination of virulent pathogenic bacteria is another. From this point of view, this paper summarizes first the mechanisms of conjugation and transformation, two important processes of horizontal gene transfer, and then discusses the approaches for disarming virulent pathogenic bacteria, that is, virulence factor inhibitors. In contrast to antibiotics, anti-virulence drugs do not impose a high selective pressure on a bacterial population, and repress the dissemination of antibiotic resistance and virulence genes. Disarmed virulence factors make virulent pathogens avirulent bacteria or pathobionts, so that we human will be able to coexist with these disarmed bacteria peacefully.

Comparative Genomic Analysis of 19 Clinical Isolates of Tigecycline-Resistant Acinetobacter baumannii

To assess the genomic profiles of tigecycline (Tgc)-resistant Acinetobacter baumannii, including antibiotic resistance (AR) genes and virulence factors (VF), whole-genome shotgun sequencing was performed on 19 Tgc-resistant (TgcR) A. baumannii strains collected in a tertiary hospital during the early phase of the clinical introduction of Tgc in China from late 2012 to mid-2014. The major sample types containing TgcR strains were sputum and drain fluid. Data from an average of 624 Mbp of sequence was generated on each bacterial genome, with Q30 quality of 90%, and an average coverage of 96.6%. TCDC-AB0715 was used as a reference genome. The genome sequences were annotated for functional elements including AR genes, VFs, genome islands, and inserted sequences before they were comparatively analyzed. The antibiotic susceptibility phenotypes of the strains were examined by a broth microdilution method to determine the minimal inhibitory concentration (MIC) of strains against major clinical antibiotics. The AR genes (ARGs) were annotated using the Comprehensive Antibiotic Resistance Database (CARD). Thirty-three ARGs were shared by all 19 TgcR strains, and 24 ARGs were distributed differently among strains. A total of 391 VFs were found to be diversely distributed in all TgcR strains. Based on ARG number distribution, the 19 TgcR strains were divided into several groups. Highly differentiated genes included gpi, mphG, armA, msrE, adec, catB8, aadA, sul1, bla_OXA–435, aph3i, and bla_TEM–1, which may represent gene markers for TgcR A. baumannii sub-types. In addition, when compared with Tgc-sensitive (TgcS) strains collected during the same period, TgcR strains featured enrichment of ARGs including aph6id, aph3ib, and teta. Compared with 26 other whole-genome sequences of A. baumannii deposited in GeneBank, TgcR strains in this study commonly lacked the EF-Tu mutation for elfamycin resistance. Previous investigation of three A. baumannii strains isolated from one patient indicated genomic exchange and a homologous recombination event associated with generation of tigecycline resistance. This study further analyzed additional TgcR strains. Phylogenetic analysis revealed a close evolutionary relationship between 19 TgcR strains and to isolates in East and Northeast China. In short, the comprehensive functional and comparative genomic analysis of 19 clinical TgcR A. baumannii strains isolated in the early stage of Tgc usage in China revealed their close phylogenetic relationship yet variable genetic background involving multiple resistance mechanisms. Using a simple ARG or VF gene number diversity method and marker genes, TgcR strain sub-types can be identified. The distinct characteristics of TgcR A. baumannii strains with versatile genomic resistance and regulation patterns raise concern regarding prediction and control of Tgc resistance in the clinic.

Cationic Peptidopolysaccharide with an Intrinsic AIE Effect for Combating Bacteria and Multicolor Imaging

An antibacterial polymer peptidopolysaccharide (COS-AMP) that integrates antibacterial and detection functions is constructed with a simple synthetic method. The COS-AMP is constructed by simulating the structure of peptidoglycan of the bacterial cell wall with chitooligosaccharide with intrinsic aggregation-induced emission (AIE) effect as the main chain, as well as a peptide polymer grafted onto its amino group. Based on the AIE effect and excitation-dependent fluorescence of COS-AMP, it is tentatively applied to multicolor imaging and quantification of bacteria. This multicolor imaging helps to match different excitation sources of fluorescent instrument for straightforward imaging and detection. The structural similarity with the bacterial cell wall component facilitates the passage of COS-AMP across the cell wall and destroys the bacterial structure, thus it has a good broad-spectrum antibacterial activity. In addition, aromatic fluorophores are not needed, and excellent biocompatibility will make it have broad application prospects.

Phytochemical Curcumin-Coformulated, Silver-Decorated Melanin-like Polydopamine/Mesoporous Silica Composites with Improved Antibacterial and Chemotherapeutic Effects against Drug-Resistant Cancer Cells

The devastating occurrence of drug resistance such as antimicrobial resistance has aroused global concerns for public health, which has propelled a continuous pursuit of safe and effective therapeutic agents. In this study, silver nanoparticles were decorated in mesoporous silica of SBA-15 coated with melanin-like polydopamine (PDA) as nanocarriers. Meanwhile, the constructed mesopore was loaded with phytochemical curcumin (CCM) through its noncovalent interactions with PDA coatings. The obtained CCM@SBA-15/PDA/Ag composites were characterized by physicochemical methods and exhibited desirable biocompatibility and low hemolytic activity. The dual-stimuli-responsive (pH and ROS) release of curcumin and/or silver nanoparticles from the CCM@SBA-15/PDA/Ag composites was achieved to reduce the side effects of noncontrolled drug leakage under physiological conditions. Additionally, compared with that of SBA-15/PDA/Ag and CCM@SBA-15/PDA, CCM@SBA-15/PDA/Ag combination showed a prolonged inhibitory effect on bacterial growth of G^- E. coli (72 h) and G⁺ S. aureus (24 h), attributing to the enhanced effect of the bactericide of silver nanoparticles and curcumin. Furthermore, through the utilization of the nanoformulation of curcumin, improved chemotherapeutic efficiency against human cervical cancer cells (HeLa) and Taxol-resistant nonsmall cell lung cells (A549/TAX) was identified in comparison with that of free curcumin. Thus, our study rationalized the combinational design of the natural compound and silver nanoparticles as an integrated dual-responsive nanoplatform in dealing with infectious bacteria and drug resistance in cancers for enhanced therapy.

In vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii

Objectives

Widespread antimicrobial resistance often limits the availability of therapeutic options to only a few last-resort drugs that are themselves challenged by emerging resistance and adverse side effects. Apramycin, an aminoglycoside antibiotic, has a unique chemical structure that evades almost all resistance mechanisms including the RNA methyltransferases frequently encountered in carbapenemase-producing clinical isolates. This study evaluates the in vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii, and provides a rationale for its superior antibacterial activity in the presence of aminoglycoside resistance determinants.

Methods

A thorough antibacterial assessment of apramycin with 1232 clinical isolates from Europe, Asia, Africa and South America was performed by standard CLSI broth microdilution testing. WGS and susceptibility testing with an engineered panel of aminoglycoside resistance-conferring determinants were used to provide a mechanistic rationale for the breadth of apramycin activity.

Results

MIC distributions and MIC₉₀ values demonstrated broad antibacterial activity of apramycin against Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Morganella morganii, Citrobacter freundii, Providencia spp., Proteus mirabilis, Serratia marcescens and A. baumannii. Genotypic analysis revealed the variety of aminoglycoside-modifying enzymes and rRNA methyltransferases that rendered a remarkable proportion of clinical isolates resistant to standard-of-care aminoglycosides, but not to apramycin. Screening a panel of engineered strains each with a single well-defined resistance mechanism further demonstrated a lack of cross-resistance to gentamicin, amikacin, tobramycin and plazomicin.

Conclusions

Its superior breadth of activity renders apramycin a promising drug candidate for the treatment of systemic Gram-negative infections that are resistant to treatment with other aminoglycoside antibiotics.

Curcumin Nanoparticles Improved Diabetic Wounds Infected With Methicillin-Resistant Staphylococcus aureus Sensitized With HAMLET

Accurately orchestrated course of events normally observed in healing are not followed in diabetic wounds, and bacterial colonization/infection further messes up the process. Novel therapeutic options for treatment of infections caused by multidrug-resistant Staphylococcus aureus are urgently needed. HAMLET (human α-lactalbumin made lethal to tumor cells) has been reported to be able to sensitize bacterial pathogens to traditional antimicrobial agents. The aim was to assess the wound healing activity of curcumin nanoparticles in diabetic wounds infected with methicillin-resistant Staphylococcus aureus (MRSA) sensitized with HAMLET. Fifty male rats were randomized into 5 groups of 10 animals each. In CONTROL group, 0.1-mL sterile saline 0.9% solution was added to the wounds with no infection. In MRSA group, the wounds were infected with MRSA and only treated with 0.1-mL sterile saline 0.9% solution. In MRSA/HAMLET group, infected wounds were treated with HAMLET (100 µg). In MRSA/CNP group, animals with infected wounds were treated with 0.1 mL topical application of 1 mg/mL curcumin nanoparticles. In MRSA/CNP/HAMLET group, animals with infected wounds were treated with topical application of 0.1 mL solution of curcumin nanoparticles (1 mg/mL) and HAMLET (100 µg). All test formulations were applied for 10 days, twice a day, starting from first treatment. Microbiological examination; planimetric, biochemical, histological, and quantitative morphometric studies; immunohistochemical staining for angiogenesis; determination of hydroxyproline levels; and reverse transcription polymerase chain reaction for caspase 3, Bcl-2, and p53 showed that there was significant difference between animals in MRSA/CNP/HAMLET group compared with other groups (P < .05). Curcumin nanoparticles improved diabetic wounds infected with MRSA sensitized with HAMLET and had the potential to offer more attention to this safer agent for topical use in infected diabetic wounds.

Synthesized Geopolymers Adsorb Bacterial Proteins, Toxins, and Cells

Pore-forming and hemolytic toxins are bacterial cytotoxic proteins required for virulence in many pathogens, including staphylococci and streptococci, and are notably associated with clinical manifestations of disease. Inspired by adsorption properties of naturally occurring aluminosilicates, we engineered inexpensive, laboratory-synthesized, aluminosilicate geopolymers with controllable pore and surface characteristics to remove pathogenic or cytotoxic material from the surrounding environment. In this study, macroporous and mesoporous geopolymers were produced with and without stearic acid surface modifications. Geopolymer binding efficacies were assessed by measuring adsorption of methicillin-resistant Staphylococcus aureus (MRSA) culture filtrate proteins, α-hemolysin and streptolysin-O toxins, MRSA whole cells, and antibiotics. Macroporous and mesoporous geopolymers were strong non-selective adsorbents for bacterial protein, protein toxins, and bacteria. Although some geopolymers adsorbed antibiotics, these synthesized geopolymers could potentially be used in non-selective adsorptive applications and optimized for adsorption of specific biomolecules.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Layer-by-Layer Decorated Nanoscale ZIF-8 with High Curcumin Loading Effectively Inactivates Gram-Negative and Gram-Positive Bacteria

Bacteria-mediated infectious diseases have become a health-care challenge globally since the development of antibiotic resistance. Reactive oxygen species produced by photosensitizers have great potential in fighting bacterial infections, especially against Gram-negative bacteria that are hard to kill by regular methods owing to their formidable defensive membrane structures under the premise of avoiding overuse of antibiotics. In this work, a small molecular photosensitizer, curcumin (CCM), was used as a model and encapsulated into zeolitic imidazolate framework-8 (ZIF-8). Then the ZIF-8 loaded with CCM (CCM@ZIF-8) was decorated with biocompatible polymers hyaluronic acid (HA) and chitosan (CS) by the layer-by-layer self-assembly technique to yeild in an antibacterial CCM@ZIF-8@HA@CS nanoparticle with a high local positive charge density and is capable of binding the surface of bacteria by electrostatic interactions. The CCM drug loading capability of the nanoparticle was found to be as high as 10.89%. Upon exposure to blue light (72 J/cm²) for 10 min, the minimum inhibitory concentration and minimum bactericidal concentration of CCM@ZIF-8@HA@CS against Gram-positive bacteria (G⁽⁺⁾) Staphylococcus aureus (S. aureus) and Gram-negative bacteria (G^(-)) Escherichia coli (E. coli) were the same, which were as low as 0.625 and 2.5 μg/mL, respectively, showing highly effective antibacterial activities. After treatment with CCM@ZIF-8@HA@CS under blue-light irradiation, the membranes of S. aureus and E. coli folded and cracked. Importantly, the antibacterial agent showed good biocompatibility in the cytotoxicity test using L929 cells and hemolysis test using rabbit blood cells under blue-light irradiation. Therefore, this CCM@ZIF-8@HA@CS nanocomposite is expected to find application in the treatment of superficial traumatic and refractory chronic infections caused by G⁽⁺⁾ and G^(-).

Efflux MexAB-Mediated Resistance in P. aeruginosa Isolated from Patients with Healthcare Associated Infections

Today, one of the most important challenges for physicians is the adequate treatment of infections due to multidrug resistant organism (MDR). Pseudomonas aeruginosa is considered an opportunistic organism causing different types of healthcare associated infections (HAIs). We aimed to investigate the MDR and pandrug resistance (PDR) rate in P. aeruginosa in our region and detect efflux-pump mexAB genes and the proposed binding interactions of five different categories of antimicrobial agents with the mexB pump. A total of 180 non-duplicated P. aeruginosa strains were isolated from patients with HAIs in the Suez Canal University Hospital. Phenotypically, minimum inhibitory concentration (MIC) was done for all MDR and PDR strains before and after addition of efflux pump inhibitor carbonyl cyanide m-chlorophenyl hydrazone (CCCP). Molecular detection of mexA and mexB genes was done by using polymerase chain reaction (PCR). Most of the isolated strains (126 strains) were MDR (70%); only 10 samples (5.5%) were PDR. MexA and mexB genes were detected in 88.2% (120 strains) and 70.5% (96 strains) of stains, respectively. All PDR strains (10 stains) carried both mexA and mexB genes. Efflux mexAB genes were detected in all MDR and PDR strains (136 strains). Molecular modeling studies were performed to investigate the modes of intermolecular binding interactions between the antimicrobial agents and mexB key amino acids that resulted in MDR and PDR. The current study reported high prevalence of MDR and PDR P. aeruginosa in patients with HAIs in the Suez Canal University Hospitals.

Strategic Moves of "Superbugs" Against Available Chemical Scaffolds: Signaling, Regulation, and Challenges

Superbugs' resistivity against available natural products has become an alarming global threat, causing a rapid deterioration in public health and claiming tens of thousands of lives yearly. Although the rapid discovery of small molecules from plant and microbial origin with enhanced bioactivity has provided us with some hope, a rapid hike in the resistivity of superbugs has proven to be the biggest therapeutic hurdle of all times. Moreover, several distinct mechanisms endowed by these notorious superbugs make them immune to these antibiotics subsequently causing our antibiotic wardrobe to be obsolete. In this unfortunate situation, though the time frame for discovering novel "hit molecules" down the line remains largely unknown, our small hope and untiring efforts injected in hunting novel chemical scaffolds with unique molecular targets using high-throughput technologies may safeguard us against these life-threatening challenges to some extent. Amid this crisis, the current comprehensive review highlights the present status of knowledge, our search for bacteria Achilles' heel, distinct molecular signaling that an opportunistic pathogen bestows to trespass the toxicity of antibiotics, and facile strategies and appealing therapeutic targets of novel drugs. Herein, we also discuss multidimensional strategies to combat antimicrobial resistance.

Pyrimidine Analogues as a New Class of Gram-Positive Antibiotics, Mainly Targeting Thymineless-Death Related Proteins

Multidrug-resistant (MDR) bacteria are widespread throughout the world and pose an increasingly serious threat to human and animal health. Besides implementing strict measures to prevent improper antibiotic use, it remains essential that novel antibiotics must be developed. These antibiotics need to exert their activity via mechanisms different from those employed by currently approved antibiotics. In this study, we used several 5-fluorouracil (5-FU) analogues as chemical probes and investigated the potential of these pyrimidine analogues as antibacterial agents. Several 5-FU derivatives exerted potent activity against strains of Gram-positive cocci (GPC) that are susceptible or resistant toward approved antibiotics, without showing cross-resistance. Furthermore, we have provided evidence that the pyrimidine analogues exerted anti-GPC activity via thymineless death by inhibition of thymidylate synthetase (ThyA) and/or inhibition of RNA synthesis. Interestingly, whole genome resequencing of in vitro-selected, pyrimidine analogue-resistant Staphylococcus aureus mutants indicated that S. aureus strains with pyrimidine-analogue resistance induced an amino acid (AA) substitution, deletion, and/or insertion into thymineless-death related proteins except for ThyA, or enhanced the ThyA transcription level. Thus, S. aureus may avoid altering the ThyA function by introducing an AA substitution, suggesting that the pyrimidine analogues, which directly bind to ThyA without phosphorylation, may be more effective and show a higher genetic barrier than the pyrimidines that depend on phosphorylation for activity. The findings of this study may assist in the future development of a novel class of antibiotics for combating MDR GPC, including methicillin-resistant S. aureus and vancomycin-resistant Enterococci.

Evaluation of plant sources for antiinfective lead compound discovery by correlating phylogenetic, spatial, and bioactivity data

Antibiotic resistance and viral diseases are rising around the world and are becoming major threats to global health, food security, and development. One measure that has been suggested to mitigate this crisis is the development of new antibiotics. Here, we provide a comprehensive evaluation of the phylogenetic and biogeographic patterns of antiinfective compounds from seed plants in one of the most species-rich regions on Earth and identify clades with naturally occurring substances potentially suitable for the development of new pharmaceutical compounds. Specifically, we combine taxonomic and phylogenetic data for >7,500 seed plant species from the flora of Java with >16,500 secondary metabolites and 6,255 georeferenced occurrence records to 1) identify clades in the phylogeny that are characterized by either an overrepresentation ("hot clades") or an underrepresentation ("cold clades") of antiinfective compounds and 2) assess the spatial patterns of plants with antiinfective compounds relative to total plant diversity across the region. Across the flora of Java, we identify 26 "hot clades" with plant species providing a high probability of finding antibiotic constituents. In addition, 24 "cold clades" constitute lineages with low numbers of reported activities but which have the potential to yield novel compounds. Spatial patterns of plant species and metabolite diversity are strongly correlated across Java, indicating that regions of highest species diversity afford the highest potential to discover novel natural products. Our results indicate that the combination of phylogenetic, spatial, and phytochemical information is a useful tool to guide the selection of taxa for efforts aimed at lead compound discovery.

Metformin Restores Tetracyclines Susceptibility against Multidrug Resistant Bacteria

Highly persistent incidence of multidrug resistant (MDR) bacterial pathogens constitutes a global burden for public health. An alternative strategy to alleviate such a crisis is to identify promising compounds to restore antibiotics activity against MDR bacteria. It is reported that the antidiabetic drug metformin exhibits the potentiation effect on tetracycline antibiotics, particularly doxycycline and minocycline, against MDR S. aureus, E. faecalis, E. coli, and S. enteritidis. Mechanistic studies demonstrate that metformin promotes intracellular accumulation of doxycycline in tetracycline-resistant E. coli. In addition, metformin boosts the immune response and alleviates the inflammatory responses in vitro. Last, metformin fully restores the activity of doxycycline in three animal infection models. Collectively, these results reveal the potential of metformin as a novel tetracyclines adjuvant to circumvent MDR bacterial pathogens and to improve the treatment outcome of recalcitrant infections.

Effect of unsymmetrical oligo-phenylene-ethynylene OPE3 against multidrug-resistant bacteria in vitro and in vivo

The rapid proliferation of multidrug-resistant (MDR) bacterial infections has posed the serious health threats. Photodynamic therapy is considered one of the most promising therapeutic strategies for combating bacterial resistance. In the present study, we synthesized an unsymmetrical oligo-p-phenylene ethynylene (OPE), namely OPE3, and investigated its antimicrobial activity against gram-negative and gram-positive MDR bacteria in vitro and in vivo. The results showed that OPE3 had marked antibacterial activity against MDR bacteria under light irradiation conditions. OPE3 exerted a slightly greater effect on gram-positive bacteria than gram-negative bacteria. Biofilm assay results showed that OPE3 could not inhibit biofilm formation at sub-minimum inhibitory concentrations (MICs), whereas a significant decrease in preformed biofilms was observed when they were treated with OPE3 at concentrations ≥2 × MIC. OPE3 had no hemolytic activity or cytotoxicity in mammalian cells at low concentrations. In the mouse model of burn infection caused by Pseudomonas aeruginosa and Staphylococcus aureus, the treatment of infected wounds with OPE3 resulted in a significant dose-dependent reduction in the bacterial load and caused smaller skin lesions. In addition, the levels of the inflammatory cytokines TNF-α and IL-6 in the serum were also significantly reduced. The present study results indicate that OPE3 may serve as a potent antimicrobial molecule for the treatment of MDR bacterial infections.

Photodegradation of Antibiotics by Noncovalent Porphyrin-Functionalized TiO2 in Water for the Bacterial Antibiotic Resistance Risk Management

Antibiotics represent essential drugs to contrast the insurgence of bacterial infections in humans and animals. Their extensive use in livestock farming, including aquaculture, has improved production performances and food safety. However, their overuse can implicate a risk of water pollution and related antimicrobial resistance. Consequently, innovative strategies for successfully removing antibiotic contaminants have to be advanced to protect human health. Among them, photodegradation TiO₂-driven under solar irradiation appears not only as a promising method, but also a sustainable pathway. Hence, we evaluated several composite TiO₂ powders with H₂TCPP, CuTCPP, ZnTCPP, and SnT4 porphyrin for this scope in order to explore the effect of porphyrins sensitization on titanium dioxide. The synthesis was realized through a fully non-covalent functionalization in water at room conditions. The efficacy of obtained composite materials was also tested in photodegrading oxolinic acid and oxytetracycline in aqueous solution at micromolar concentrations. Under simulated solar irradiation, TiO₂ functionalized with CuTCPP has shown encouraging results in the removal of oxytetracycline from water, by opening the way as new approaches to struggle against antibiotic's pollution and, finally, to represent a new valuable tool of public health.

Supramolecular Assemblies of Heterogeneous Mesoporous Silica Nanoparticles to Co-deliver Antimicrobial Peptides and Antibiotics for Synergistic Eradication of Pathogenic Biofilms

Pathogenic biofilms protected by extracellular polymeric substances frequently compromise the efficiency of antibacterial drugs and severely threaten human health. In this study, we designed a multi-stimuli-responsive magnetic supramolecular nanoplatform to co-deliver large and low molecular weight drugs for synergistic eradication of pathogenic biofilms. This co-delivery platform was composed of mesoporous silica nanoparticles (MSNs) with large pores (MSNLP) capped by β-cyclodextrin (β-CD)-modified polyethylenimine (PEICD) and adamantane (ADA)-decorated MSNs containing a magnetic core (MagNP@MSNA) capped by cucurbit[6]uril (CB[6]). The host MSNs (H, MSNLP@PEICD) and the guest MSNs (G, MagNP@MSNA-CB[6]) spontaneously form coassemblies (H+G), based on the host-guest interactions between β-CD and ADA. Under the stimulus of pathogen cells together with heating by an alternating magnetic field (AMF), the supramolecular coassemblies released both the large molecular weight antimicrobial peptide melittin (MEL) and the low molecular weight antibiotic ofloxacin (OFL) with high efficiency. As compared to free drugs (MEL and OFL) or unattached MSNs (H or G), the drug-loading H+G coassemblies (H-MEL+G-OFL) exhibited much higher capacity for biofilm eradication, thoroughly removing biofilm biomass and killing the pathogenic cells, and displaying no obvious toxicity to mammalian cells. This strong antibiofilm capacity was severely decreased when the host and guest components were prevented from coassembling but administered simultaneously, revealing the critical role of the supramolecular assembly in biofilm removal. Moreover, an in vivo implantation model showed that the coassemblies eradicated the pathogenic biofilms from the implants, preventing host tissue damage and inflammation. Therefore, the co-delivering and multi-stimuli-responsive nanocarriers could overcome the anti-infection difficulties during treatment of infections because of protective biofilms.

Formulation technologies and advances for oral delivery of novel nitroimidazoles and antimicrobial peptides

Antibiotic resistance has become a global crisis, driving the exploration for novel antibiotics and novel treatment approaches. Among these research efforts two classes of antibiotics, bicyclic nitroimidazoles and antimicrobial peptides, have recently shown promise as novel antimicrobial agents with the possibility to treat multi-drug resistant infections. However, they suffer from the issue of poor oral bioavailability due to disparate factors: low solubility in the case of nitroimidazoles (BCS class II drugs), and low permeability in the case of peptides (BCS class III drugs). Moreover, antimicrobial peptides present another challenge as they are susceptible to chemical and enzymatic degradation, which can present an additional pharmacokinetic hurdle for their oral bioavailability. Formulation technologies offer a potential means for improving the oral bioavailability of poorly permeable and poorly soluble drugs, but there are still drawbacks and limitations associated with this approach. This review discusses in depth the challenges associated with oral delivery of nitroimidazoles and antimicrobial peptides and the formulation technologies that have been used to overcome these problems, including an assessment of the drawbacks and limitations associated with the technologies that have been applied. Furthermore, the potential for supercritical fluid technology to overcome the shortcomings associated with conventional drug formulation methods is reviewed.

Capping 1,3-propanedithiol to boost the antibacterial activity of protein-templated copper nanoclusters

We have prepared copper nanoclusters (Cu NCs) in the presence of bovine serum albumin (BSA) and 1,3-propanedithiol (PDT). The PDT/BSA-Cu NCs possess great activities against different types of bacteria, including non-multidrug-resistant bacteria (Escherichia coli, Salmonella Enteritidis, Pseudomonas aeruginosa, and Staphylococcus aureus) and multidrug-resistant bacteria (methicillin-resistant S. aureus). Their minimal inhibitory concentration (MIC) values are at least 242-fold and 10-fold lower than that of the free PDT and BSA-Cu NCs, respectively. The PDT/BSA-Cu NCs are strongly bound to the bacterial membrane, in which they induce the generation of ascorbyl (Asc) and perhydroxyl (HOO) radicals that result in disruption of their membrane integrity. At a concentration of 100-fold higher than their MIC for Escherichia coli, the PDT/BSA-Cu NCs exhibit negligible cytotoxicity towards the tested mammalian cells and show insignificant hemolysis. We have further demonstrated that low-cost PDT/BSA-Cu NCs-coated carbon fiber fabrics (CFFs) are effective against antibacterial growth, showing their great potential for antifouling applications.

Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation

DNA gyrase and topoisomerase IV are well-validated pharmacological targets, and quinolone antibacterial drugs are marketed as their representative inhibitors. However, in recent years, resistance to these existing drugs has become a problem, and new chemical classes of antibiotics that can combat resistant strains of bacteria are strongly needed. In this study, we applied our hit-to-lead (H2L) chemistry for the identification of a new chemical class of GyrB/ParE inhibitors by efficient use of thermodynamic parameters. Investigation of the core fragments obtained by fragmentation of high-throughput screening hit compounds and subsequent expansion of the hit fragment was performed using isothermal titration calorimetry (ITC). The 8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative 13e showed potent activity against Escherichia coli DNA gyrase with an IC₅₀ value of 0.0017 μM. In this study, we demonstrated the use of ITC for primary fragment screening, followed by structural optimization to obtain lead compounds, which advanced into further optimization for creating novel antibacterial agents.

The antifungal pipeline: the need is established. Are there new compounds?

Our review summarizes and compares the temporal development (eras) of antifungal drug discovery as well as antibacterial ventures. The innovation gap that occurred in antibacterial discovery from 1960 to 2000 was likely due to tailoring of existing compounds to have better activity than predecessors. Antifungal discovery also faced innovation gaps. The semi-synthetic antibiotic era was followed closely by the resistance era and the heightened need for new compounds and targets. With the immense contribution of comparative genomics, antifungal targets became part of the discovery focus. These targets by definition are absolutely required to be fungal- or even lineage (clade) specific. Importantly, targets need to be essential for growth and/or have important roles in disease and pathogenesis. Two types of antifungals are discussed that are mostly in the FDA phase I–III clinical trials. New antifungals are either modified to increase bioavailability and stability for instance, or are new compounds that inhibit new targets. One of the important developments in incentivizing new antifungal discovery has been the prolific number of publications of global and country-specific incidence. International efforts that champion global antimicrobial drug discovery are discussed. Still, interventions are needed. The current pipeline of antifungals and alternatives to antifungals are discussed including vaccines.

Antibiotics: A Bibliometric Analysis of Top 100 Classics

Citation frequencies represent the most significant contributions in any respective field. This bibliometric analysis aimed to identify and analyze the 100 most-cited publications in the field of antibiotics and to highlight the trends of research in this field. “All databases” of Clarivate Analytics’ Web of Science was used to identify and analyze the 100 publications. The articles were then cross-matched with Scopus and Google Scholar. The frequency of citation ranged from 940 to 11,051 for the Web of Science, 1053 to 10,740 for Scopus, and 1162 to 20,041 for Google Scholar. A total of 513 authors made contributions to the ranked list, and Robert E.W. Hancock contributed in six articles, which made it to the ranked list. Sixty-six scientific contributions originated from the United States of America. Five publications were linked to the University of Manitoba, Canada, that was identified as the educational organization, made the most contributions (n = 5). According to the methodological design, 26 of the most cited works were review-type closely followed by 23 expert opinions/perspectives. Eight articles were published in Nature journal, making it the journal with the most scientific contribution in this field. Correlation analysis between the publication age and citation frequency was found statistically significant (p = 0.012).

Gene editing in dermatology: Harnessing CRISPR for the treatment of cutaneous disease

The discovery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has revolutionized gene editing research. Through the repurposing of programmable RNA-guided CRISPR-associated (Cas) nucleases, CRISPR-based genome editing systems allow for the precise modification of specific sites in the human genome and inspire novel approaches for the study and treatment of inherited and acquired human diseases. Here, we review how CRISPR technologies have stimulated key advances in dermatologic research.  We discuss the role of CRISPR in genome editing for cutaneous disease and highlight studies on the use of CRISPR-Cas technologies for genodermatoses, cutaneous viruses and bacteria, and melanoma. Additionally, we examine key limitations of current CRISPR technologies, including the challenges these limitations pose for the widespread therapeutic application of CRISPR-based therapeutics.

Identification of the Molecular Determinants Involved in Antimicrobial Activity of Pseudodesmin A, a Cyclic Lipopeptide From the Viscosin Group

Cyclic lipo(depsi)peptides (CLiPs) from Pseudomonas constitute a class of natural products involved in a broad range of biological functions for their producers. They also display interesting antimicrobial potential including activity against Gram-positive bacteria. Literature has indicated that these compounds can induce membrane permeabilization, possibly through pore-formation, leading to the general view that the cellular membrane constitutes the primary target in their mode of action. In support of this view, we previously demonstrated that the enantiomer of pseudodesmin A, a member of the viscosin group of CLiPs, shows identical activity against a test panel of six Gram-positive bacterial strains. Here, a previously developed total organic synthesis route is used and partly adapted to generate 20 novel pseudodesmin A analogs in an effort to derive links between molecular constitution, structure and activity. From these, the importance of a macrocycle closed by an ester bond as well as a critical length of β-OH fatty acid chain capping the N-terminus is conclusively demonstrated, providing further evidence for the importance of peptide-membrane interactions in the mode of action. Moreover, an alanine scan is used to unearth the contribution of specific amino acid residues to biological activity. Subsequent interpretation in terms of a structural model describing the location and orientation of pseudodesmin A in a membrane environment, allows first insight in the peptide-membrane interactions involved. The biological screening also identified residue positions that appear less sensitive to conservative modifications, allowing the introduction of a non-perturbing tryptophan residue which will pave the way toward biophysical studies using fluorescence spectroscopy.

Genome mining as a biotechnological tool for the discovery of novel marine natural products

Compared to terrestrial environments, the oceans harbor a variety of environments, creating higher biodiversity, which gives marine natural products a high occurrence of significant biology and novel chemistry. However, traditional bioassay-guided isolation and purification strategies are severely limiting the discovery of additional novel natural products from the ocean. With an increasing number of marine microorganisms being sequenced, genome mining is gradually becoming a powerful tool to retrieve novel marine natural products. In this review, we have summarized genome mining approaches used to analyze key enzymes of biosynthetic pathways and predict the chemical structure of new gene clusters by introducing successful stories that used genome mining strategy to identify new marine-derived compounds. Furthermore, we also put forward challenges for genome mining techniques and their proposed solutions. The detailed analysis of the genome mining strategy will help researchers to understand this novel technique and its application. With the development of a genome sequence, genome mining strategies will be applied more widely, which will drive rapid development in the field of marine natural product development.

Light-Excited Antibiotics for Potentiating Bacterial Killing via Reactive Oxygen Species Generation

The irrational or excessive use of antibiotics causes the emergence of bacterial resistance, making antibiotics less effective or ineffective. As the number of resistant antibiotics increases, it is crucial to develop new strategies and innovative approaches to potentiate the efficacy of existing antibiotics. In this paper, we report that some existing antibiotics can produce reactive oxygen species (ROS) directly under light irradiation. Thus, a novel antibacterial photodynamic therapy (PDT) strategy is proposed by using existing antibiotics for which the activities are potentiated via light-activation. This antibiotic-based PDT strategy can achieve efficient bacteria killing with a low dosage of antibiotics, indicating that bacterial killing can be enhanced by the light-irradiated antibiotics. Moreover, the specific types of ROS produced by different antibiotics under light irradiation were studied for better elucidation of the antibacterial mechanism. The findings can extend the application of existing antibiotics and provide a promising strategy for treatment of bacterial infections and even cancers.

Natural Compounds as Pharmaceuticals: The Key Role of Cytochromes P450 Reactivity

The design of drugs from natural products is a re-emerging area due to the need for bioactive compounds. The exploitation of natural products and their derivatives obtained by biocatalysis is in line with the higher attention given today to new sustainable technologies that better preserve the environment (green chemistry). The research field of cytochromes P450 (CYPs) is continuously providing new enzymes and mutants that produce metabolites suitable for late-stage functionalization for new potential drugs. This review provides an overview of the exploitation of CYPs as biocatalysts in drug synthesis. Additionally, recent progress in protein and metabolic engineering is provided to show how these enzymes offer a toolbox that can be combined with other biocatalytic or chemical processes to build new platforms for the green production of new drugs.

Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer

Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).

Development of Staphylococcus Enzybiotics: The Ph28 Gene of Staphylococcus epidermidis Phage PH15 Is a Two-Domain Endolysin

Given the worldwide increase in antibiotic resistant bacteria, bacteriophage derived endolysins represent a very promising new alternative class of antibacterials in the fight against infectious diseases. Endolysins are able to degrade the prokaryotic cell wall, and therefore have potential to be exploited for biotechnological and medical purposes. Staphylococcus epidermidis is a Gram-positive multidrug-resistant (MDR) bacterium of human skin. It is a health concern as it is involved in nosocomial infections. Genome-based screening approach of the complete genome of Staphylococcus virus PH15 allowed the identification of an endolysin gene (Ph28; NCBI accession number: YP_950690). Bioinformatics analysis of the Ph28 protein predicted that it is a two-domain enzyme composed by a CHAP (22-112) and MurNAc-LAA (171-349) domain. Phylogenetic analysis and molecular modelling studies revealed the structural and evolutionary features of both domains. The MurNAc-LAA domain was cloned, and expressed in E. coli BL21 (DE3). In turbidity reduction assays, the recombinant enzyme can lyse more efficiently untreated S. epidermidis cells, compared to other Staphylococcus strains, suggesting enhanced specificity for S. epidermidis. These results suggest that the MurNAc-LAA domain from Ph28 endolysin may represent a promising new enzybiotic.

Role of respiratory NADH oxidation in the regulation of Staphylococcus aureus virulence

The success of Staphylococcus aureus as a pathogen is due to its capability of fine-tuning its cellular physiology to meet the challenges presented by diverse environments, which allows it to colonize multiple niches within a single vertebrate host. Elucidating the roles of energy-yielding metabolic pathways could uncover attractive therapeutic strategies and targets. In this work, we seek to determine the effects of disabling NADH-dependent aerobic respiration on the physiology of S. aureus. Differing from many pathogens, S. aureus has two type-2 respiratory NADH dehydrogenases (NDH-2s) but lacks the respiratory ion-pumping NDHs. Here, we show that the NDH-2s, individually or together, are not essential either for respiration or growth. Nevertheless, their absence eliminates biofilm formation, production of α-toxin, and reduces the ability to colonize specific organs in a mouse model of systemic infection. Moreover, we demonstrate that the reason behind these phenotypes is the alteration of the fatty acid metabolism. Importantly, the SaeRS two-component system, which responds to fatty acids regulation, is responsible for the link between NADH-dependent respiration and virulence in S. aureus.

From Substrate to Fragments to Inhibitor Active In Vivo against Staphylococcus aureus

Antibiotic resistance is a worldwide threat due to the decreasing supply of new antimicrobials. Novel targets and innovative strategies are urgently needed to generate pathbreaking drug compounds. NAD kinase (NADK) is essential for growth in most bacteria, as it supports critical metabolic pathways. Here, we report the discovery of a new class of antibacterials that targets bacterial NADK. We generated a series of small synthetic adenine derivatives to screen those harboring promising substituents in order to guide efficient fragment linking. This led to NKI1, a new lead compound inhibiting NADK that showed in vitro bactericidal activity against Staphylococcus aureus. In a murine model of infection, NKI1 restricted survival of the bacteria, including methicillin-resistant S. aureus. Collectively, these findings identify bacterial NADK as a potential drug target and NKI1 as a lead compound in the treatment of staphylococcal infections.

Host Defense Peptide Mimicking Peptide Polymer Exerting Fast, Broad Spectrum, and Potent Activities toward Clinically Isolated Multidrug-Resistant Bacteria

Multidrug-resistant (MDR) bacteria have emerged quickly and have caused serious nosocomial infections. It is urgent to develop novel antimicrobial agents for treating MDR bacterial infections. In this study, we isolated 45 strains of bacteria from hospital patients and found shockingly that most of these strains were MDR to antimicrobial drugs. This inspired us to explore antimicrobial peptide polymers as synthetic mimics of host defense peptides in combating drug-resistant bacteria and the formidable antimicrobial challenge. We found that peptide polymer 80:20 DM:Bu (where DM is a hydrophilic/cationic subunit and Bu is a hydrophobic subunit) displayed fast bacterial killing, broad spectrum, and potent activity against clinically isolated strains of MDR bacteria. Moreover, peptide polymer 80:20 DM:Bu displayed potent in vivo antibacterial efficacy, comparable to the performance of polymyxin B, in a Pseudomonas aeruginosa (P. aeruginosa) infected rat full-thickness wound model. The peptide polymer can be easily synthesized from ring-opening polymerization with remarkable reproducibility in structural properties and biological activities. The peptide polymer's potent and broad spectrum antimicrobial activities against MDR bacteria in vitro and in vivo, resistance to proteolysis, and high structural diversity altogether imply a great potential of peptide polymer 80:20 DM:Bu in antimicrobial applications as synthetic mimics of host defense peptides.