Optimizing Antimicrobial Peptide Dendrimers in Chemical Space

We used nearest‐neighbor searches in chemical space to improve the activity of the antimicrobial peptide dendrimer (AMPD) G3KL and identified dendrimer T7 , which has an expanded activity range against Gram‐negative pathogenic bacteria including Klebsiellae pneumoniae, increased serum stability, and promising activity in an in vivo infection model against a multidrug‐resistant strain of Acinetobacter baumannii. Imaging, spectroscopic studies, and a structural model from molecular dynamics simulations suggest that T7 acts through membrane disruption. These experiments provide the first example of using virtual screening in the field of dendrimers and show that dendrimer size does not limit the activity of AMPDs.     

Combining Topology and Sequence Design for the Discovery of Potent Antimicrobial Peptide Dendrimers against Multidrug‐Resistant Pseudomonas aeruginosa

Multidrug‐resistant opportunistic bacteria, such as Pseudomonas aeruginosa, represent a major public health threat. Antimicrobial peptides (AMPs) and related peptidomimetic systems offer an attractive opportunity to control these pathogens. AMP dendrimers (AMPDs) with high activity against multidrug‐resistant clinical isolates of P. aeruginosa and Acinetobacter baumannii were now identified by a systematic survey of the peptide sequences within the branches of a distinct type of third‐generation peptide dendrimers. Combined topology and peptide sequence design as illustrated here represents a new and general strategy to discover new antimicrobial agents to fight multidrug‐resistant bacterial pathogens.     

Exploring the resistance mechanism of imipenem in carbapenem hydrolysing class D beta-lactamases OXA-143 and its variant OXA-231 (D224A) expressing Acinetobacter baumannii: An in-silico approach

Acinetobacter baumannii (A. baumannii), is a Gram negative, coccobacilli and is associated with nosocomial infections. The bacterium has developed resistance to all known classes of antibiotics. Multi-drug resistant A. baumannii infections have been treated with the carbapenem group of antibiotics like imipenem and meropenem. Recent reports indicate that A. baumannii has acquired resistance to imipenem due to the secretion of carbapenem hydrolysing class D beta-lactamases (CHDLs). Such CHDLs found in carbapenem resistant A. baumannii belongs to OXA-143 and its variant OXA-231, which has Alanine (A) in place of Aspartic acid (D) at sequence position 224. The mutation of the OXA-231 CHDL alters the catalytic activity of the enzyme. Hence, the present study was carried out to find the probable mechanism of imipenem resistance in OXA-143 and OXA-231 (D224A) CHDLs expressing A. baumannii by employing molecular docking and dynamics. Methods Our study reveals that OXA-143 CHDL-imipenem complex has more binding affinity than OXA-231 (D224A) CHDL-imipenem complex. Our results indicate that there is a strong binding affinity of OXA-143 with imipenem when compared with OXA-243 and this mechanism might be the probable reason for imipenem resistance in OXA-143 expressing A. baumannii strains.     

Synthesis and investigation of binding interactions of 1,4-benzoxazine derivatives on topoisomerase IV in Acinetobacter baumannii$

Abstract

Acinetobacter baumannii has emerged as an important pathogen for nosocomial infections having high morbidity and mortality. This pathogen is notorious for antimicrobial resistance to many common antimicrobial agents including fluoroquinolones, which have both intrinsic and acquired resistance mechanisms. Fluoroquinolones targeting the bacterial topoisomerase II (DNA gyrase and Topo IV) show potent broad-spectrum antibacterial activity by the stabilization of the covalent enzyme–DNA complex. However, their efficacy is now being threatened by an increasing prevalence of resistance. Fluoroquinolones cause stepwise mutations in DNA gyrase and Topo IV, having alterations of their binding sites. Furthermore, the water–Mg⁺² bridge, which provides enzyme–fluoroquinolone interactions, has a significant role in resistance. In this study, 13 compounds were synthesized as 1,4-benzoxazine derivatives which act as bacterial topoisomerase II inhibitors and their antibacterial activities were determined against multi-drug resistant Acinetobacter strains which have ciprofloxacin (CIP) resistant and GyrA mutation. Afterwards we performed docking studies with Topo IV (pdb:2XKK) of these compounds to comprehend their binding properties in Discovery Studio 3.5. The results of this study show significant conclusions to elucidate the resistance mechanism and lead to the design of new antibacterial agents as bacterial topoisomerase II inhibitors.     

Stereoselective Synthesis of the O-antigen of A. baumannii ATCC 17961 Using Long-Range Levulinoyl Group Participation

Herein, we described the first synthesis of the pentasaccharide and decasaccharide of the A. baumannii ATCC 17961 O-antigen for developing a synthetic carbohydrate-based vaccine against A. baumannii infection. The efficient synthesis of the rare sugar 2,3-diacetamido-glucuronate was achieved using our recently introduced organocatalytic glycosylation method. We found, for the first time, that long-range levulinoyl group participation via a hydrogen bond can result in a significantly improved β-selectivity in glycosylations. This solves the stereoselectivity problem of highly branched galactose acceptors. The proposed mechanism was supported by control experiments and DFT computations. Benefiting from the long-range levulinoyl group participation strategy, the pentasaccharide donor and acceptor were obtained via an efficient [2+1+2] one-pot glycosylation method and were used for the target decasaccharide synthesis.     

Mechanism and Kinetics of Carbon Dioxide Capture Using Activated 2‐Amino‐2‐methyl‐1,3‐propanediol

The continued use of fossil fuels as primary sources of energy in industry and other applications stands the test of time, due to their availability and relatively lower cost than alternative sources of energy. In view of this perspective, obtaining an advanced bulk carbon dioxide (CO₂) capture medium becomes an urgent necessity so as to mitigate their effect, especially in global warming, as the use of fossil fuels produces a high rate of CO₂. In this work, the mechanism and kinetics of CO₂ capture using aqueous piperazine (PZ) as an activator to 2‐amino‐2‐methyl‐1,3‐propanediol (AMPD) were investigated. The termolecular mechanism was used to model the kinetics of the system. Reaction kinetics of the single pure amines was first obtained. The reaction rate constant, the k value of AMPD, was 77.2 m³/kmol·s, with a reaction order, n, of 1.25 at 298 K. while that of PZ was equal to 11,059 m³/kmol·s and n as 1.49 at 298 K. Blending of 0.05 kmol/m³ of PZ with 0.5 kmol/m³ of AMPD gave a rate constant, k, value of 23,319 m³/kmol·s and n equal to 1.23 at 298 K. The result obtained for the blended system is more than twice the value of the summation of the corresponding pure amines; in addition, it is comparably higher than the rate constant of monoethanolamine (MEA) in use as a commercial solvent for CO₂ capture. Therefore, an aqueous blend of PZ with AMPD deserves more comprehensive study as a solvent for commercial CO₂ capture. AMPD like other sterically hindered amines absorbs CO₂ in an equimolar ratio that is significantly higher than that of MEA. PZ serves as a promoter in the amine mixture and is required in a very small proportion.     

Rational design of inhibitors against LpxA protein of Acinetobacter baumannii using a virtual screening method

BackgroundAcinetobacter baumannii is a highly antimicrobial resistant nosocomial pathogen. Resistance to currently used antibiotics has limited effective drugs against this bacterium. This study aimed to propose a rational inhibitor design against the LpxA protein of A. baumannii using a virtual screening method based on a similar structure of ligands.MethodsIn this study, we targeted LpxA protein, which is involved in the early stage of LPS biosynthesis. In the next step, we used Peptide920 and 1,2- Ethanediol as templates to find similar compounds using Drugbank and Zinc15 webservers, respectively. Subsequently, molecular dynamics (MD) simulations were carried out for LpxA protein and two complexes of ZINC895081 and Macrolactam-1 which represented the highest binding affinity and best conformation. Finally, ADMET properties, water solubility and drug-likeness of the desired compounds were evaluated using SwissADME and DruLiTo softwares.ResultsAccording to considered criteria, Drugbank suggested 5 compunds including Ilomastat, Macrolactam-1, Macrolactam-2, Macimorelin, and Oglufanide. On the other hand, Zinc15 webserver suggested 4 compunds including ZINC895048, ZINC895081, ZINC901061 and ZINC1531008. The result of the HDOCK server and Molegro virtual docker (MVD) showed that Macrolactam-1 and ZINC895081 (Citrate) had the highest docking score. In addition, MD simulations showed that ZINC895081 and Macrolactam-1 ligands have the stable binding to the LpxA protein. According to Lipinski's rule, these two compounds are non-carcinogenic, non-toxic and promising inhibitors against LpxA of A. baumannii.ConclusionIt seems that Macrolactam-1 and ZINC895081 (Citrate) are two valuable promising inhibitors against the LpxA protein of A. baumannii. Further in vitro and in vivo experiments are needed to confirm the capabilities of these proposed compounds against A. baumannii.     

Profiling of Potential Antibacterial Compounds of Lactic Acid Bacteria against Extremely Drug Resistant (XDR) Acinetobacter baumannii

A total of 20 of isolates of lactic acid bacteria (LAB) were selected and screened for antagonistic activity against clinical strains of 30 clinical isolates of extremely drug-resistant (XDR) Acinetobacter baumannii using the well diffusion assay method. Results showed that 50% of the highly LAB strains possessed inhibitory activity against (up to 66%) of the XDR A. baumannii strains tested. The supernatant of the twenty LAB strains was subjected to gas chromatography mass spectrometry (GCMS) revealed that the common compound found in the active isolates against XDR A. baumannii was 3-Isobutyl-2,3,6,7,8,8a-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione, a known potential diketopiperazine group. The molecular docking study against potential antibacterial targets with selected ligands was performed to predict the binding mode of interactions, which is responsible for antibacterial activity. The docking analysis of the potent compounds supported the potential antibacterial activity exhibiting high inhibition constant and binding affinity in silico.     

Controlling Antibacterial Activity Exclusively with Visible Light: Introducing a Tetra-ortho-Chloro-Azobenzene Amino Acid

The introduction of a novel tetra-ortho-chloroazobenzene amino acid (CEBA) has enabled photoswitching of the antimicrobial activity of tyrocidine A analogues by using exclusively visible light, granting spatiotemporal control under benign conditions. Compounds bearing this photoswitchable amino acid become active upon irradiation with red light, but quickly turn-off upon exposure to other visible light wavelengths. Critically, sunlight quickly triggers isomerisation of the red light-activated compounds into their original trans form, offering an ideal platform for self-deactivation upon release into the environment. Linear analogues of tyrocidine A were found to provide the best photocontrol of their antimicrobial activity, leading to compounds active against Acinetobacter baumannii upon isomerisation. Exploration of their N- and C-termini has provided insights into key elements of their structure and has allowed obtaining new antimicrobials displaying excellent strain selectivity and photocontrol.     

Mapping of the Modular Closthioamide Architecture Reveals Crucial Motifs of Polythioamide Antibiotics

Closthioamide, the first known secondary metabolite from an anaerobic microorganism (Clostridium cellulolyticum), represents a highly potent antibiotic that is active against methicillin‐resistant Staphylococcus aureus (MRSA) and vancomycin‐resistant Enterococcus faecalis (VRE) at nanomolar concentrations. To unveil structure–activity relationships of the unusual polythioamide natural product we have designed a synthetic grid to access analogues with altered terminal aromatic moieties, diverse p‐phenyl substituents, different types and sizes of aliphatic spacers, varying numbers of thioamide residues, and diverse sizes and symmetries of the poly‐β‐thioalanyl backbone. A library of 28 closthioamide analogues was tested against a panel of human pathogenic bacteria. We found that aromatic terminal groups, the defined length of the spacer groups, the presence of all six thioamide residues and the modular arrangement of the β‐thioalanyl units play essential roles for the antibiotic activity of closthioamide, yet there is a degree of freedom in the symmetry of the molecule. This study yields the first insights into pivotal structural motifs and the structural space of this new family of antibiotics, a prerequisite for the development of these promising antibiotics.     

More Than Just Light: Clinical Relevance of Light Perception in the Nosocomial Pathogen Acinetobacter baumannii and Other Members of the Genus Acinetobacter

A summary of the major findings concerning light modulation in Acinetobacter baumannii, which governs aspects related to the success of this microorganism as a nosocomial pathogen, is presented. Particularly, the evidence shows that light modulates the ability of the bacteria to persist in the environment, its virulence against eukaryotic hosts and even susceptibility to certain antibiotics. The light signal is sensed through different mechanisms, in some cases involving specialized photoreceptors of the BLUF‐type, whereas in others, directly by a photosensitizer molecule. We also provide new data concerning the genomic context of BLUF‐domain containing proteins within the genus Acinetobacter, as well as further insights into the mechanism of light‐mediated reduction in susceptibility to antibiotics. The overall information points toward light being a crucial stimulus in the lifestyle of members of the genus Acinetobacter as well as in other clinically relevant species, such as members of the ESKAPE group, playing therefore an important role in the clinical settings.     

Antibacterial and antibiofilm activity of nanochelating based silver nanoparticles against several nosocomial pathogens

The emergence of multi‐drug resistant (MDR) bacteria and dynamic pattern of infectious diseases demand to develop alternative and more effective therapeutic strategies. Silver nanoparticles (AgNPs) are among the most widely commercialized engineered nanomaterials, because of their unique properties and increasing use for various applications in nanomedicine. This study for the first time aimed to evaluate the antibacterial and antibiofilm activities of newly synthesized nanochelating based AgNPs against several Gram‐positive and ‐negative nosocomial pathogens. Nanochelating technology was used to design and synthesize the AgNPs. The cytotoxicity was tested in human cell line using the MTT assay. AgNPs minimal inhibitory concentration (MIC) was determined by standard broth microdilution. Antibiofilm activity was assayed by a microtiter‐plate screening method. The two synthesized AgNPs including AgNPs (A) with the size of about 20‐25 nm, and AgNPs (B) with 30‐35 nm were tested against Staphylococcus aureus, Staphylococcus epidermidis, Acinetobacter baumannii, and Pseudomonas aeruginosa. AgNPs exhibited higher antibacterial activity against Gram‐positive strains. AgNPs were found to significantly inhibit the biofilm formation of tested strains in concentration 0.01 to 10 mg/mL. AgNPs (A) showed significant effective antibiofilm activity compared to AgNPs (B). In summary, our results showed the promising antibacterial and antibiofilm activity of our new nanochelating based synthesized AgNPs against several nosocomial pathogens.     

Preparation,Characterization and Antimicrobial Properties of Nanosized Silver-Containing Carbon/Silica Composites from Rice Husk Waste

Rice husk, one of the main side products in the rice production, and its sustainable management represent a challenge in many countries. Herein, we describe the use of this abundant agricultural bio-waste as feedstock for the preparation of silver-containing carbon/silica nano composites with antimicrobial properties. The synthesis was performed using a fast and cheap methodology consisting of wet impregnation followed by pyrolysis, yielding C/SiO₂ composite materials doped with varying amounts of silver from 28 to 0.001 wt %. The materials were fully characterized and their antimicrobial activity against ESKAPE pathogens, namely E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and E. coli, and the pathogenic yeast C. albicans was investigated. Sensitivities of these strains against the prepared materials were demonstrated, even with exceptional low amounts of 0.015 m% silver. Hence, we report a straightforward method for the synthesis of antimicrobial agents from abundant sources which addresses urgent questions like bio-waste valorization and affordable alternatives to increasingly fewer effective antibiotics.     

Regulation of 5'-adenosine monophosphate deaminase in the freeze tolerant wood frog, Rana sylvatica

Background

The wood frog, Rana sylvatica, is one of a few vertebrate species that have developed natural freeze tolerance, surviving days or weeks with 65–70% of its total body water frozen in extracellular ice masses. Frozen frogs exhibit no vital signs and their organs must endure multiple stresses, particularly long term anoxia and ischemia. Maintenance of cellular energy supply is critical to viability in the frozen state and in skeletal muscle, AMP deaminase (AMPD) plays a key role in stabilizing cellular energetics. The present study investigated AMPD control in wood frog muscle.

Results

Wood frog AMPD was subject to multiple regulatory controls: binding to subcellular structures, protein phosphorylation, and effects of allosteric effectors, cryoprotectants and temperature. The percentage of bound AMPD activity increased from 20 to 35% with the transition to the frozen state. Bound AMPD showed altered kinetic parameters compared with the free enzyme (S _0.5 AMP was reduced, Hill coefficient fell to ~1.0) and the transition to the frozen state led to a 3-fold increase in S _0.5 AMP of the bound enzyme. AMPD was a target of protein phosphorylation. Bound AMPD from control frogs proved to be a low phosphate form with a low S _0.5 AMP and was phosphorylated in incubations that stimulated PKA, PKC, CaMK, or AMPK. Bound AMPD from frozen frogs was a high phosphate form with a high S _0.5 AMP that was reduced under incubation conditions that stimulated protein phosphatases. Frog muscle AMPD was activated by Mg·ATP and Mg·ADP and inhibited by Mg·GTP, KCl, NaCl and NH₄Cl. The enzyme product, IMP, uniquely inhibited only the bound (phosphorylated) enzyme from muscle of frozen frogs. Activators and inhibitors differentially affected the free versus bound enzyme. S _0.5 AMP of bound AMPD was also differentially affected by high versus low assay temperature (25 vs 5°C) and by the presence/absence of the natural cryoprotectant (250 mM glucose) that accumulates during freezing.

Conclusion

Maintenance of long term viability under the ischemic conditions in frozen muscle requires attention to the control of cellular energetics. Differential regulatory controls on AMPD by mechanisms including binding to muscle proteins, actions allosteric effectors, glucose and temperature effects and reversible phosphorylation adjust enzyme function for an optimal role in controlling cellular adenylate levels in ischemic frozen muscle. Stable modification of AMPD properties via freeze-responsive phosphorylation may contribute both to AMPD control and to coordinating AMPD function with other enzymes of energy metabolism in cold ischemic muscle.     

Inhibition of Beta-Lactamase by 1,4-Naphthalenedione from the Plant <Emphasis Type="Italic">Holoptelea integrifolia</Emphasis>

The most important mechanism of the beta-lactam antibiotic resistance is the destruction of the antibiotics by the enzyme beta-lactamase. Use of beta-lactamase inhibitors in combination with antibiotics is one of the successful antibacterial strategies. The inhibitory effect of a phytochemical, 1,4-naphthalenedione, isolated from the plant Holoptelea integrifolia on beta-lactamase is reported here. This compound was found to have a synergistic effect with the antibiotic amoxicillin against a resistant strain of Staphylococcus aureus. The enzyme was purified from the organism and incubated with the compound. An assay showed that the compound can inhibit the enzymatic activity of beta-lactamase. Modeling and molecular docking studies indicated that the compound can fit into the active site of beta-lactamase. Hence, the compound can serve as a potential lead compound for the development of effective beta-lactamase inhibitor that can be used against beta-lactam-resistant microbial strains.     

Synthesis,crystal structures,and antimicrobial activity of square-planar chloride and isocyanate Ni(II) complexes with the condensation product of 2-(diphenylphosphino)benzaldehyde and Girard’s T reagent

Square-planar isocyanate and chloride Ni(II) complexes with tridentate PNO condensation product of 2-(diphenylphosphino)benzaldehyde and Girard’s T reagent have been synthesized and their crystal structures were determined. These Ni(II) complexes with different monodentate ligands, chloride, cyanate, and thiocyanate were tested for their antimicrobial activities against pathogenic microorganisms. The ligand and Ni(II) complexes were active not only against laboratory control strains of bacteria and yeast, but also on clinical isolates of Escherichia coli and Pseudomonas aeruginosa strains resistant to most of the clinically used antibiotics.     

Synthesis and Characterization of Disulfide-Schiff Base Derivatives and <Emphasis Type="Italic">in vitro</Emphasis> Investigation of Their Antibacterial Activity Against Multidrug-Resistant <Emphasis Type="Italic">Acinetobacter baumannii</Emphasis> Isolates: A New Study

In this study two different methods without a catalyst and with a CeO₂ nano catalyst were used for the synthesis of dimeric disulfide-Schiff bases. The dimeric disulfide-Schiff base derivatives were characterized by FT-IR, NMR, and MS spectra, and elemental analysis. The disulfide-Schiff bases and their derivatives 2–5c were screened for in vitro antibacterial activity against 40 multidrug-resistant strains of Acinetobacter baumannii, and their minimum inhibitory concentrations were determined. Most of products exhibited high antibacterial activity against Acinetobacter baumannii.     

Multiplex identification of sepsis‐causing Gram‐negative pathogens from the plasma of infected blood

Early and accurate detection of bacterial pathogens in the blood is the most crucial step for sepsis management. Gram‐negative bacteria are the most common organisms causing severe sepsis and responsible for high morbidity and mortality. We aimed to develop a method for rapid multiplex identification of clinically important Gram‐negative pathogens and also validated whether our system can identify Gram‐negative pathogens with the cell‐free plasm DNA from infected blood. We designed five MLPA probe sets targeting the genes specific to major Gram‐negative pathogens (uidA and lacY for E. coli, ompA for A. baumannii, phoE for K. pneumoniae, and ecfX for P. aeruginosa) and one set targeting the CTX‐M group 1 to identify the ESBL producing Gram‐negative pathogens. All six target‐specific peaks were clearly separated without any non‐specific peaks in a multiplex reaction condition. The minimum detection limit was 100 fg of pathogen DNA. When we tested 28 Gram‐negative clinical isolates, all of them were successfully identified without any non‐specific peaks. To evaluate the clinical applicability, we tested seven blood samples from febrile patients. Three blood culture positive cases showed E. coli specific peaks, while no peak was detected in the other four culture negative samples. This technology can be useful for detection of major sepsis‐causing, drug‐resistant Gram‐negative pathogens and also the major ESBL producing Gram‐negatives from the blood of sepsis patients in a clinical setting. This system can help early initiation of effective antimicrobial treatment against Gram‐negative pathogens for sepsis patients, which is very crucial for better treatment outcomes.     

Total Syntheses of Conjugation-Ready Repeating Units of Acinetobacter baumannii AB5075 for Glycoconjugate Vaccine Development

Acinetobacter baumannii is an opportunistic pathogen that causes serious nosocomial infections. One of the multidrug-resistant strains, AB5075, can result in bacteremia, pneumonia and wound infections associated with high morbidity and mortality. The structurally unique glycans on the surface of these bacteria are attractive targets for the development of glycoconjugate vaccines. Here, we report the first total synthesis of the densely functionalized trisaccharide repeating unit of A. baumannii AB5075 as well as two analogues. The construction of 1,2-cis linkages between the rare sugars relies on a double-serial inversion strategy. The judicious selection of building blocks and reaction conditions allowed for stereoselective glycosylations, the installation of acetamido groups and the (S)-3-hydroxybutanoyl chain.     

Synthesis and Antifungal Activity of Substituted 2‐Aryl Benzimidazoles Derivatives

Benzimidazole fungicides were among the early systemic fungicides developed and used for controlling a wide variety of plant diseases. During the course of our screening process for active compounds, two 2‐aryl benzimidazoles derivatives bearing sulfoxide group ( 6b and 6c ) have been demonstrated to exhibit good inhibition activity against high‐resistant isolate of Botrytis cinerea compared with carbendazim, and the inhibition rates are up to 46.67% and 51.11% at the concentration of 10 μg/mL, which might be considered as the active framework for the discovery of novel fungicide to high‐resistant isolate of B. cinerea.