DNA gyrase as a drug target

Metagenomics Analysis Reveals the Composition and Functional Differences of Fecal Microbiota in Wild, Farm, and Released Chinese Three-Keeled Pond Turtles (Mauremys reevesii)

The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota's composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species.

Antimicrobial potential, GCMS analysis and molecular docking studies of Coelogyne suaveolens extracts: Identification of bioactive compounds with mechanism of action

Coelogyne suaveolens has been used as a traditional medicine for many years, and its potential as a natural source of antibacterial agents is of great interest. This investigation aimed to identify the bioactive compounds in the plant extract and assess their antibacterial properties. To achieve this, we identified the bioactive compounds using Gas chromatography mass spectrometry (GCMS) analysis on the extract's ethyl acetate fraction and used the disc diffusion method to determine the antibacterial effect. Additionally, molecular docking were performed to predict the binding affinities of selected phytochemicals against specific proteins in order to identify the root cause of bacterial inhibition. Our results revealed that the extract exhibited significant antibacterial activity against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae, which are common and problematic pathogens. Furthermore, molecular docking studies identified eight best-selected compounds, of which {androstan-17-one, oxime, (5.alpha.)-}, diethofencarb, tetraconazole, {3,6-dimethyl-2,3,3a,4,5,7a-hexahydrobenzofuran}, and geranyl acetate showed a significant binding affinity with best binding interaction with the target enzymes. This suggests that binding to these specific proteins might lead to the mechanism of action of the evaluated antibacterial action. In conclusion, the present study contributes to the growing body of knowledge on natural antimicrobial agents and could have significant implications for the development of new and effective antibacterial agents.

Nano-enabled antimicrobial thin films: design and mechanism of action

Antimicrobial thin films are types of protective coatings that are applied to surfaces such as medical devices, food packaging materials, water-resistant coatings, and other systems. These films prevent and reduce the spread of microbial organisms, including bacteria, fungi, and viruses. Antimicrobial thin films can be prepared from a variety of nanostructured materials including metal nanoparticles, metal oxides, plant materials, enzymes, bacteriocins and polymers. Their antimicrobial mechanism varies mostly based on the types of active agents from which the film is made of. Antimicrobial thin films are becoming increasingly popular microbial treatment methods due to their advantages such as enhanced stability, reduced toxicity levels, extended effectiveness over time and broad spectrum antimicrobial action without side effects on human health or the environment. This popularity and enhanced performance is mainly due to the extended possibility of film designs. Thin films offer convenient formulation methods which makes them suitable for commercial practices aiming at high turnover rates along with residential applications requiring frequent application cycles. This review focuses on recent developments in the possible processing methods and design approaches for assembling the various types of antimicrobial materials into nanostructured thin film-based delivery systems, along with mechanisms of action against microbes.

Plasmodium falciparum topoisomerases: Emerging targets for anti-malarial therapy

Different metabolic pathways like DNA replication, transcription, and recombination generate topological constrains in the genome. These topological constraints are resolved by essential molecular machines known as topoisomerases. To bring changes in DNA topology, the topoisomerases create a single or double-stranded nick in the template DNA, hold the nicked ends to let the tangled DNA pass through, and finally re-ligate the breaks. The DNA nicking and re-ligation activities as well as ATPase activities (when present) in topoisomerases are subjected to inhibition by several anticancer and antibacterial drugs, thus establishing these enzymes as successful targets in anticancer and antibacterial therapies. The anti-topoisomerase drugs interfere with the functioning of these enzymes and result in the accumulation of DNA tangles or lethal genomic breaks, thereby promoting host cell (or organism) death. The potential of topoisomerases in the human malarial parasite, Plasmodium falciparum in antimalarial drug development has received little attention so far. Interestingly, the parasite genome encodes orthologs of topoisomerases found in eukaryotes, prokaryotes, and archaea, thus, providing an enormous opportunity for investigating these enzymes for antimalarial therapeutics. This review focuses on the features of Plasmodium falciparum topoisomerases (PfTopos) with respect to their closer counterparts in other organisms. We will discuss overall advances and basic challenges with topoisomerase research in Plasmodium falciparum and our attempts to understand the interaction of PfTopos with classical and new-generation topoisomerase inhibitors using in silico molecular docking approach. The recent episodes of parasite resistance against artemisinin, the only effective antimalarial drug at present, further highlight the significance of investigating new drug targets including topoisomerases in antimalarial therapeutics.

The effects of Pandanus tectorius leaf extract on the resistance of White-leg shrimp Penaeus vannamei towards pathogenic Vibrio parahaemolyticus

Pandanus tectorius leaf extract effect on the White-leg shrimp Penaeus vannamei tolerance against Vibrio parahaemolyticus were investigated in this study. Thirty shrimp post-larvae measured at approximately 1 cm were exposed for 24 h to 0.5, 1, 2, 3, 4, 5 and 6 g/L leaf extract and subsequently observed for survival and immune-related genes expression (Hsp70, ProPO, peroxinectin, penaeidin, crustin and transglutaminase), followed by determination of their tolerance and histological tissue profiles upon Vibrio challenge. Survival of shrimps treated with 6 g/L of leaf extract improved by up to 95% to controls. Hsp70, crustin, and prophenoloxidase mRNA levels were observed to be 8.5, 10.4, and 1.5-fold higher, respectively. Histopathological analysis of the hepatopancreas and the muscle tissues revealed major tissue degeneration in Vibrio-challenged shrimps but not in shrimps primed with P. tectorius leaf extract. Of all the dose examined, the best pathogen resistance results were obtained with a 24 h incubation of shrimp in 6 g/L P. tectorius methanolic leaf extract. The tolerance towards V. parahaemolyticus might be associated with the increased regulation of Hsp70, prophenoloxidase and crustin upon exposure to the extract, all immune-related proteins essential for pathogen elimination in Penaeid shrimp. The present study primarily demonstrated that P. tectorius leaf extract is a viable alternative for enhancing P. vannamei post-larvae resistance against V. parahaemolyticus, a major bacterial pathogen in aquaculture.

A Fluorescence-Based, T5 Exonuclease-Amplified DNA Cleavage Assay for Discovering Bacterial DNA Gyrase Poisons

Fluoroquinolones (FQs) are potent antibiotics of clinical significance, known for their unique mechanism of action as gyrase poisons, which stabilize gyrase-DNA cleavage complexes and convert gyrase into a DNA-damaging machinery. Unfortunately, FQ resistance has emerged, and these antibiotics can cause severe side effects. Therefore, discovering novel gyrase poisons with different chemical scaffolds is essential. The challenge lies in efficiently identifying them from compound libraries containing thousands or millions of drug-like compounds, as high-throughput screening (HTS) assays are currently unavailable. Here we report a novel fluorescence-based, T5 exonuclease-amplified DNA cleavage assay for gyrase poison discovery. This assay capitalizes on recent findings showing that multiple gyrase molecules can simultaneously bind to a plasmid DNA molecule, forming multiple gyrase-DNA cleavage complexes on the same plasmid. These gyrase-DNA cleavage complexes, stabilized by a gyrase poison, can be captured using sarkosyl. Proteinase K digestion results in producing small DNA fragments. T5 exonuclease, selectively digesting linear and nicked DNA, can fully digest the fragmented linear DNA molecules and, thus, "amplify" the decrease in fluorescence signal of the DNA cleavage products after SYBR Green staining. This fluorescence-based, T5 exonuclease-amplified DNA cleavage HTS assay is validated using a 50-compound library, making it suitable for screening large compound libraries.

Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum

The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.

Identification of potential Escherichia coli DNA gyrase B inhibitors targeting antibacterial therapy: an integrated docking and molecular dynamics simulation study

The alarming rise in the rate of antibiotic resistance is a matter of significant concern. DNA gyrase B (GyrB), a critical bacterial enzyme involved in DNA replication, transcription, and recombination, has emerged as a promising target for antibacterial agents. Inhibition of GyrB disrupts bacterial DNA replication, leading to cell death, making it an attractive candidate for antibiotic development. Although several classes of antibiotics targeting GyrB are currently in clinical use, the emergence of antibiotic resistance necessitates the exploration of novel inhibitors. In this study, we aimed to identify potential Escherichia coli GyrB inhibitors from a database of phytoconstituents sourced from Indian medicinal plants. Utilizing virtual screening, we performed a rigorous search to identify compounds with the most promising inhibitory properties against GyrB. Two compounds, namely Zizogenin and Cucurbitacin S, were identified based on their favorable drug likeliness and pharmacokinetic profiles. Employing advanced computational techniques, we analyzed the binding interactions of Zizogenin and Cucurbitacin S with the ATP-binding site of GyrB through molecular docking simulations. Both compounds exhibited robust binding interactions, evidenced by their high docking energy scores. To assess the stability of these interactions, we conducted extensive 100 ns molecular dynamics (MD) simulations, which confirmed the stability of Zizogenin and Cucurbitacin S when bound to GyrB. In conclusion, our study highlights Zizogenin and Cucurbitacin S as promising candidates for potential antibacterial agents targeting GyrB. Experimental validation of these compounds is warranted to further explore their efficacy and potential as novel antibiotics to combat antibiotic-resistant bacteria.Communicated by Ramaswamy H. Sarma.

Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera

Introduction

The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes.

Methods

Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil.

Results

Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H₂O₂ and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1.

Discussion

These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.

Synthesis, Structure, Hirshfeld Surface Analysis, Non-Covalent Interaction, and In Silico Studies of 4-Hydroxy-1-[(4-Nitrophenyl)Sulfonyl]Pyrrolidine-2-Carboxyllic Acid

The new compound 4-hydroxy-1-[(4-nitrophenyl)sulfonyl]pyrrolidine-2-carboxyllic acid was obtained by the reaction of 4-hydroxyproline with 4-nitrobenzenesulfonyl chloride. The compound was characterized using single crystal X-ray diffraction studies. Spectroscopic methods including NMR, FTIR, ES-MS, and UV were employed for further structural analysis of the synthesized compound. The title compound was found to have crystallized in an orthorhombic crystal system with space group P212121. The S1-N1 bond length of 1.628 (2) Å was a strong indication of the formation of the title compound. The absence of characteristic downfield 1H NMR peak of pyrrolidine ring and the presence of S-N stretching vibration at 857.82 cm-1 on the FTIR are strong indications for the formation of the sulfonamide. The experimental study was complemented with computations at the B3LYP/6-311G +  + (d,p) level of theory to gain more understanding of interactions in the compound at the molecular level. Noncovalent interaction, Hirsfeld surface analysis and interaction energy calculations were employed in the analysis of the supramolecular architecture of the compound. Predicted ADMET parameters, awarded suitable bioavailability credentials, while the molecular docking study indicated that the compound enchants promising inhibition prospects against dihydropteroate synthase, DNA topoisomerase, and SARS-CoV-2 spike.

Graphical Abstract

Herein we present the solid state structure, noncovalent interaction and spectroscopic analysis of a prospective bioactive compound 4-hydroxy-1-[(4-nitrophenyl)sulphonyl]pyrrolidine-2-carboxyllic acid.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10870-023-00978-0.

Novel and Structurally Diversified Bacterial DNA Gyrase Inhibitors Discovered through a Fluorescence-Based High-Throughput Screening Assay

Bacterial DNA gyrase, a type IIA DNA topoisomerase that plays an essential role in bacterial DNA replication and transcription, is a clinically validated target for discovering and developing new antibiotics. In this article, based on a supercoiling-dependent fluorescence quenching (SDFQ) method, we developed a high-throughput screening (HTS) assay to identify inhibitors targeting bacterial DNA gyrase and screened the National Institutes of Health's Molecular Libraries Small Molecule Repository library containing 370,620 compounds in which 2891 potential gyrase inhibitors have been identified. According to these screening results, we acquired 235 compounds to analyze their inhibition activities against bacterial DNA gyrase using gel- and SDFQ-based DNA gyrase inhibition assays and discovered 155 new bacterial DNA gyrase inhibitors with a wide structural diversity. Several of them have potent antibacterial activities. These newly discovered gyrase inhibitors include several DNA gyrase poisons that stabilize the gyrase-DNA cleavage complexes and provide new chemical scaffolds for the design and synthesis of bacterial DNA gyrase inhibitors that may be used to combat multidrug-resistant bacterial pathogens. Additionally, this HTS assay can be applied to screen inhibitors against other DNA topoisomerases.

Abundant antibiotic resistance genes in rhizobiome of the human edible Moringa oleifera medicinal plant

Moringa oleifera (or the miracle tree) is a wild plant species widely grown for its seed pods and leaves, and is used in traditional herbal medicine. The metagenomic whole genome shotgun sequencing (mWGS) approach was used to characterize antibiotic resistance genes (ARGs) of the rhizobiomes of this wild plant and surrounding bulk soil microbiomes and to figure out the chance and consequences for highly abundant ARGs, e.g., mtrA, golS, soxR, oleC, novA, kdpE, vanRO, parY, and rbpA, to horizontally transfer to human gut pathogens via mobile genetic elements (MGEs). The results indicated that abundance of these ARGs, except for golS, was higher in rhizosphere of M. oleifera than that in bulk soil microbiome with no signs of emerging new soil ARGs in either soil type. The most highly abundant metabolic processes of the most abundant ARGs were previously detected in members of phyla Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and Firmicutes. These processes refer to three resistance mechanisms namely antibiotic efflux pump, antibiotic target alteration and antibiotic target protection. Antibiotic efflux mechanism included resistance-nodulation-cell division (RND), ATP-binding cassette (ABC), and major facilitator superfamily (MFS) antibiotics pumps as well as the two-component regulatory kdpDE system. Antibiotic target alteration included glycopeptide resistance gene cluster (vanRO), aminocoumarin resistance parY, and aminocoumarin self-resistance parY. While, antibiotic target protection mechanism included RbpA bacterial RNA polymerase (rpoB)-binding protein. The study supports the claim of the possible horizontal transfer of these ARGs to human gut and emergence of new multidrug resistant clinical isolates. Thus, careful agricultural practices are required especially for plants used in circles of human nutrition industry or in traditional medicine.

Fucoxanthin’s Optimization from Undaria pinnatifida Using Conventional Heat Extraction, Bioactivity Assays and In Silico Studies

Brown macroalgae are a potential source of natural pigments. Among them, Undaria pinnatifida is recognized for its high concentration of fucoxanthin (Fx), which is a pigment with a wide range of bioactivities. In this study, three independent parameters were optimized for conventional heat extraction (CHE) to maximize the recovery of Fx from Undaria pinnatifida. Optimal conditions (temperature = 45 °C, solvent = 70%, and time = 61 min) extracted 5.1 mg Fx/g dw. Later, the bioactivities of the Fx-rich extracts (antioxidant, antimicrobial, and neuroprotective) were assessed using in vitro and in silico approaches. In vitro assays indicated that Fx has a strong antioxidant capacity and even stronger antimicrobial activity against gram-positive bacteria. This data was supported in silico where Fx established a high binding affinity to DR, a Staphylococcus aureus protein, through aa ALA-8, LEU-21, and other alkane interactions. Finally, the in vitro enzymatic inhibition of AChE using Fx, was further supported using docking models that displayed Fx as having a high affinity for aa TYR72 and THR 75; therefore, the Fx extraction behavior explored in this work may reduce the costs associated with energy and solvent consumption. Moreover, this paper demonstrates the efficiency of CHE when recovering high amounts of Fx from Undaria pinnatifida. Furthermore, these findings can be applied in different industries.

Antimicrobial Activities of Salacia oblonga Wall Leaf and Root Extracts Against Different Bacterial Strains and Fungal Isolates

Antibiotic resistance and the hazardous nature of synthetic drugs is threatening issue in the health sector. The alternative for this problem is to focus on plants that attribute to various compounds that exhibit therapeutic properties. Therefore, the study aims to evaluate the antimicrobial efficacy of Salacia oblonga leaf and root extracts against tested human pathogens. The S. oblonga extracts showed a significant zone of inhibition against bacteria and fungi. The leaf and root extracts of S. oblonga are prepared using low polar to high polar solvents in the Soxhlet apparatus and tested on the selected bacterial and fungal strains. Agar well diffusion and broth dilution methods evaluate antibacterial activity, antifungal activity, and Minimum Inhibitory Concentration (MIC) of extracts. Among the extracts tested, the ethyl acetate extract of root showed more antimicrobial activity against the tested bacterial and fungal strains. The most susceptible bacterial and fungal species against ethyl acetate extract are Micrococcus luteus, Mycobacterium tuberculosis, Microsporum canis, Trichophyton interdigitale, and Microsporum gypseum. The MIC for bacteria ranged from 13.0 to > 200 µg/ml, whereas for fungi, the MIC ranged from 25.9 to > 200 µg/ml. Ethyl acetate extract of root with 100 µg/ml concentration showed 29.1 mm and 28.7 mm zone of inhibition against bacterial strains M. luteus and M. tuberculosis, respectively. The ethyl acetate extract of root with a 100 µg/ml concentration showed 15.8, 15.2, and 15.6 mm zone of inhibition against fungal isolates M. canis, T. interdigitale, and M. gypseum, respectively. The activity of root and leaf extracts increased in a concentration-dependent manner, and further, the compounds isolated from the crude extracts of leaf and root showed antimicrobial activity. Structural elucidation of isolated compounds Lambertic acid and Ferruginol was done using NMR spectroscopy. Reports indicate that Lambertic acid was isolated previously, but the isolation of hydroxy Ferruginol from S. oblonga leaf extract was reported unprecedented.

Role of unique loops in oligomerization and ATPase function of Plasmodium falciparum gyrase B

DNA gyrase is an ATP dependent Type IIA topoisomerase that is unique to prokaryotes. Interestingly DNA gyrase has also been found in the apicoplasts of apicomplexan parasites like Plasmodium falciparum (Pf) the causative agent of Malaria. Gyrase B (GyrB), a subunit of gyrase A₂ B₂ complex has an N-terminal domain (GyrBN) which is endowed with ATPase activity. We reported earlier that PfGyrB exhibits ATP-independent dimerization unlike its bacterial counterparts. Here we report the role of two unique regions (L1 and L2) identified in PfGyrBN. Deletions of L1 alone (PfGyrBNΔL1), or L1 and L2 together (PfGyrBNΔL1ΔL2) have indicated that these regions may play an important role in ATPase activity and the oligomeric state of PfGyrBN. Our experiments show that the deletion of L1 region disrupts the dimer interface of PfGyrBN and reduces its ATPase activity. Further through ITC experiments we show that the binding affinity of ATP to PfGyrBN is reduced upon the deletion of L1 region. We have observed a reduction in ATPase activity for of all three proteins PfGyrBN, PfGyrBNΔL1, and PfGyrBNΔL1ΔL2 in presence of coumermycin. Our results suggests that L1 region of PfGyrBN is likely to be functionally important and may provide a unique dimer interface that affects its enzymatic activity. Since deletion of L1 region decreases the affinity of ATP to the protein, this region can be targeted toward designing novel inhibitors of ATP hydrolysis.

DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases

Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.

Anti-vibrio and immune-enhancing activity of medicinal plants in shrimp: A comprehensive review

Disease epidemics in shrimp aquaculture increase apace with the development of aquaculture systems throughout the world. The disease caused by Vibrio spp. (vibriosis) is considered the most devastating, which has made it the most feared bacterial disease in the shrimp sector. In aquaculture, several strategies have already been applied to control Vibrio strains, including chemicals, probiotics, antibiotics, natural products from plants, including plant oils; hence, there has been considerable attention for using plants in shrimp aquaculture to provide sustainable, eco-friendly and safe compounds, such as alkaloids, saponins, terpenoids and flavonoids for replacing chemical compounds and antibiotics in current aquaculture. Medicinal plants may also have immunostimulating activity, increase growth and resistance in shrimps. The present paper aims to review the inhibition of Vibrio spp. in shrimp by medicinal plants, using both in vitro or/and in vivo techniques. Several medicinal plants appear capable of inhibiting growth of Vibrio pathogens outside living shrimp or in the body of shrimp, through enhancing growth and immune capacity when shrimps are fed or injected with them. In the current review Gracilaria spp. (Gracilariaceae family) and Sargassum spp. (family Sargassaceae) have been used most for in vitro and in vivo experiments. Among the terrestrial plants, Eucalyptus camaldulensis, Psidium guajava, Rhodomyrtus tomentosa, and Syzygium cumini (Myrtaceae family) had significant activity against Vibrio.

Towards Advances in Medicinal Plant Antimicrobial Activity: A Review Study on Challenges and Future Perspectives

The increasing incidence of drug- resistant pathogens raises an urgent need to identify and isolate new bioactive compounds from medicinal plants using standardized modern analytical procedures. Medicinal plant-derived compounds could provide novel straightforward approaches against pathogenic bacteria. This review explores the antimicrobial activity of plant-derived components, their possible mechanisms of action, as well as their chemical potential. The focus is put on the current challenges and future perspectives surrounding medicinal plants antimicrobial activity. There are some inherent challenges regarding medicinal plant extracts and their antimicrobial efficacy. Appropriate and optimized extraction methodology plant species dependent leads to upgraded and selective extracted compounds. Antimicrobial susceptibility tests for the determination of the antimicrobial activity of plant extracts may show variations in obtained results. Moreover, there are several difficulties and problems that need to be overcome for the development of new antimicrobials from plant extracts, while efforts have been made to enhance the antimicrobial activity of chemical compounds. Research on the mechanisms of action, interplay with other substances, and the pharmacokinetic and/or pharmacodynamic profile of the medicinal plant extracts should be given high priority to characterize them as potential antimicrobial agents.

Identification of novel topoisomerase II alpha inhibitors by virtual screening, molecular docking, and bioassay

Breast cancer is one of the most common tumors, and its treatment still leaves room for improvement. Topoisomerase II alpha is a potential target for the treatment of human diseases such as breast cancer. In this article, we attempted to discover a novel anticancer drug. We have used the topoisomerase II alpha protein-Homo sapiens (Human) to hierarchically screen the Maybridge database. Based on their docking score, the top hit compounds have been assayed for inhibition in a topoisomerase II pBR322 DNA relaxation assay in vitro. Candidate compound 6 (CP6) was found to have the best inhibitory effect for topoisomerase II among the 20 tested compounds. In addition, CP6 had potent cytotoxicity against eight tested tumor cell lines. At the same time, CP6 was shown to have potential anti-multidrug resistance capabilities. This study identifies CP6, which can contribute to the development of new topoisomerase II inhibitors as anticancer agents.

Benzohydrazide and Phenylacetamide Scaffolds: New Putative ParE Inhibitors

Antibacterial resistance (ABR) is a major life-threatening problem worldwide. Rampant dissemination of ABR always exemplified the need for the discovery of novel compounds. However, to circumvent the disease, a molecular target is required, which will lead to the death of the bacteria when acted upon by a compound. One group of enzymes that have proved to be an effective target for druggable candidates is bacterial DNA topoisomerases (DNA gyrase and ParE). In our present work, phenylacetamide and benzohydrazides derivatives were screened for their antibacterial activity against a selected panel of pathogens. The tested compounds displayed significant antibacterial activity with MIC values ranging from 0.64 to 5.65 μg/mL. Amongst 29 title compounds, compounds 5 and 21 exhibited more potent and selective inhibitory activity against Escherichia coli with MIC values at 0.64 and 0.67 μg/mL, respectively, and MBC at onefold MIC. Furthermore, compounds exhibited a post-antibiotic effect of 2 h at 1× MIC in comparison to ciprofloxacin and gentamicin. These compounds also demonstrated the concentration-dependent bactericidal activity against E. coli and synergized with FDA-approved drugs. The compounds are screened for their enzyme inhibitory activity against E. coli ParE, whose IC₅₀ values range from 0.27 to 2.80 μg/mL. Gratifyingly, compounds, namely 8 and 25 belonging to the phenylacetamide series, were found to inhibit ParE enzyme with IC₅₀ values of 0.27 and 0.28 μg/mL, respectively. In addition, compounds were benign to Vero cells and displayed a promising selectivity index (169.0629-951.7240). Moreover, compounds 1, 7, 8, 21, 24, and 25 (IC₅₀: <1 and Selectivity index: >200) exhibited potent activity in reducing the E. coli biofilm in comparison with ciprofloxacin, erythromycin, and ampicillin. These astonishing results suggest the potential utilization of phenylacetamide and benzohydrazides derivatives as promising ParE inhibitors for treating bacterial infections.

Mechanistic Insight into Antimicrobial and Antioxidant Potential of Jasminum Species: A Herbal Approach for Disease Management

Drug resistance among microbial pathogens and oxidative stress caused by reactive oxygen species are two of the most challenging global issues. Firstly, drug-resistant pathogens cause several fatalities every year. Secondly aging and a variety of diseases, such as cardiovascular disease and cancer, are associated with free radical generated oxidative stress. The treatments currently available are limited, ineffective, or less efficient, so there is an immediate need to tackle these issues by looking for new therapies to resolve resistance and neutralize the harmful effects of free radicals. In the 21st century, the best way to save humans from them could be by using plants as well as their bioactive constituents. In this specific context, Jasminum is a major plant genus that is used in the Ayurvedic system of medicine to treat a variety of ailments. The information in this review was gathered from a variety of sources, including books, websites, and databases such as Science Direct, PubMed, and Google Scholar. In this review, a total of 14 species of Jasminum have been found to be efficient and effective against a wide variety of microbial pathogens. In addition, 14 species were found to be active free radical scavengers. The review is also focused on the disorders related to oxidative stress, and it was concluded that Jasminum grandiflorum and J. sambac normalized various parameters that were elevated by free radical generation. Alkaloids, flavonoids (rutoside), terpenes, phenols, and iridoid glucosides are among the main phytoconstituents found in various Jasminum species. Furthermore, this review also provides insight into the mechanistic basis of drug resistance, the generation of free radicals, and the role of Jasminum plants in combating resistance and neutralizing free radicals.

Thiosemicarbazide Derivatives Decrease the ATPase Activity of Staphylococcus aureus Topoisomerase IV, Inhibit Mycobacterial Growth, and Affect Replication in Mycobacterium smegmatis

Compounds targeting bacterial topoisomerases are of interest for the development of antibacterial agents. Our previous studies culminated in the synthesis and characterization of small-molecular weight thiosemicarbazides as the initial prototypes of a novel class of gyrase and topoisomerase IV inhibitors. To expand these findings with further details on the mode of action of the most potent compounds, enzymatic studies combined with a molecular docking approach were carried out, the results of which are presented herein. The biochemical assay for 1-(indol-2-oyl)-4-(4-nitrophenyl) thiosemicarbazide (4) and 4-benzoyl-1-(indol-2-oyl) thiosemicarbazide (7), showing strong inhibitory activity against Staphylococcus aureus topoisomerase IV, confirmed that these compounds reduce the ability of the ParE subunit to hydrolyze ATP rather than act by stabilizing the cleavage complex. Compound 7 showed better antibacterial activity than compound 4 against clinical strains of S. aureus and representatives of the Mycobacterium genus. In vivo studies using time-lapse microfluidic microscopy, which allowed for the monitoring of fluorescently labelled replisomes, revealed that compound 7 caused an extension of the replication process duration in Mycobacterium smegmatis, as well as the growth arrest of bacterial cells. Despite some similarities to the mechanism of action of novobiocin, these compounds show additional, unique properties, and can thus be considered a novel group of inhibitors of the ATPase activity of bacterial type IIA topoisomerases.

DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis

DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA-topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single-molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA-associated proteins, supporting the idea that they often function as part of multi-enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini-A. These new findings are advancing our understanding of DNA-related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.

Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain

DNA Gyrase is a type II topoisomerase that utilizes the energy of ATP hydrolysis for introducing negative supercoils in DNA. The protein comprises two subunits GyrA and GyrB that form a GyrA₂GyrB₂ heterotetramer. GyrB subunit contains the N-terminal domain (GBNTD) for ATPase activity and the C-terminal domain (GBCTD) for interaction with GyrA and DNA. Earlier structural studies have revealed three different conformational states for GBNTD during ATP hydrolysis defined as open, semi-open, and closed. Here we report, the three-dimensional structure of a new transient closed conformation of GBNTD from Salmonella Typhi (StGBNTD) at 1.94 Å resolution. Based on the structural analysis of this transient closed conformation, we propose the role of protein in the mechanism of ATP hydrolysis. We further explored the effect of pH on ATPase activity and structural stability of the GBNTD using CD and fluorescence spectroscopy at varying pH environment. Kinetic parameters obtained from the ATPase assay were correlated with its secondary and tertiary structure at their respective pH environment. The protein possessed maximum ATPase activity and structural stability at optimum pH 8. At acidic pH, a remarkable decrease in both enzymatic activity and structural stability was observed whereas at alkaline pH there was no significant change. The structural analysis of StGBNTD reveals the role of polar interactions in stabilizing the overall dimeric conformation of the protein.

DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines

DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA. These enzymes are widely conserved, sharing >91% amino acid identity between the closely related species Escherichia coli and Salmonella enterica serovar Typhimurium. Why, then, do E. coli and Salmonella exhibit different DNA supercoiling when experiencing the same conditions? We now report that this surprising difference reflects disparate activation of their DNA gyrases by the polyamine spermidine and its precursor putrescine. In vitro, Salmonella DNA gyrase activity was sensitive to changes in putrescine concentration within the physiological range, whereas activity of the E. coli enzyme was not. In vivo, putrescine activated the Salmonella DNA gyrase and spermidine the E. coli enzyme. High extracellular Mg2+ decreased DNA supercoiling exclusively in Salmonella by reducing the putrescine concentration. Our results establish the basis for the differences in global DNA supercoiling between E. coli and Salmonella, define a signal transduction pathway regulating DNA supercoiling, and identify potential targets for antibacterial agents.

Antibacterial evaluation and molecular docking studies of pyrazole-thiosemicarbazones and their pyrazole-thiazolidinone conjugates

A library of pyrazole-thiazolidinone conjugates was synthesized using a molecular hybridization approach through a Vilsmeier-Haack reaction. The compounds were tested for anti-microbial activity against two Gram-positive bacteria (Staphylococcus aureus and methicillin-resistant Staphylococcus aureus) and four Gram-negative bacteria (Escherichia coli, Salmonella typhimurium, Klebsiella pneumonia and Pseudomonas aeruginosa). Among the compounds tested, 3-((2,4-dichlorophenyl)-1-(2,4-dinitrophenyl)-1H-pyrazol-yl)methylene)hydrazinecarbothioamide (3a) and 2-((3-(2-chlorophenyl)-1-(2,4 dinitrophenyl)-1H-pyrazol-4-yl)methyleneamino)thiazolidin-4-one (4b) emerged as the most potent anti-microbial compounds with minimum bactericidal concentrations of < 0.2 µM against MRSA and S. aureus. Structure-activity relationship analysis further revealed that the presence of 2,4-dichloro moiety surprisingly influenced the activity of the compounds. Molecular docking studies of the compounds into the crystal structure of topoisomerase II and topoisomerase IV suggest that compounds 3a and 4b preferably interact with the targets through hydrogen bonding.

Photocatalytic and bactericidal properties and molecular docking analysis of TiO2 nanoparticles conjugated with Zr for environmental remediation

Despite implementing several methodologies including a combination of physical, chemical and biological techniques, aquatic and microbial pollution remains a challenge to this day. Recently, nanomaterials have attracted considerable attention due to their extraordinary prospective for utilization toward environmental remediation. Among several probable candidates, TiO₂ stands out due to its potential for use in multifaceted applications. One way to improve the catalytic and antimicrobial potential of TiO₂ is to dope it with certain elements. In this study, Zr-doped TiO₂ was synthesized through a sol–gel chemical method using various dopant concentrations (2, 4, 6, and 8 wt%). Surface morphological, microstructural and elemental analysis was carried out using FESEM and HR-TEM along with EDS to confirm the formation of Zr–TiO₂. XRD spectra showed a linear shift of the (101) anatase peak to lower diffraction angles (from 25.4° to 25.08°) with increasing Zr⁴⁺ concentration. Functional groups were examined via FTIR, an ample absorption band appearing between 400 and 700 cm⁻¹ in the acquired spectrum was attributed to the vibration modes of the Ti–O–Ti linkage present within TiO₂ nanoparticles, which denotes the formation of TiO₂. Experimental results indicated that with increasing dopant concentrations, photocatalytic potential was enhanced significantly. In this respect, TiO₂ doped with 8 wt% Zr (sample 0.08 : 1) exhibited outstanding performance by realizing 98% elimination of synthetic MB in 100 minutes. This is thought to be due to a decreased rate of electron–hole pair recombination that transpires upon doping. Therefore, it is proposed that Zr-doped TiO₂ can be used as an effective photocatalyst material for various environmental and wastewater treatment applications. The good docking scores and binding confirmation of Zr-doped TiO₂ suggested doped nanoparticles as a potential inhibitor against selected targets of both E. coli and S. aureus. Hence, enzyme inhibition studies of Zr-doped TiO₂ NPs are suggested for further confirmation of these in silico predictions.

Despite implementing several methodologies including a combination of physical, chemical and biological techniques, aquatic and microbial pollution remains a challenge to this day.

Kinetic Study of DNA Topoisomerases by Supercoiling-Dependent Fluorescence Quenching

DNA topoisomerases are essential enzymes for all living organisms and important targets for anticancer drugs and antibiotics. Although DNA topoisomerases have been studied extensively, steady-state kinetics has not been systematically investigated because of the lack of an appropriate assay. Previously, we demonstrated that newly synthesized, fluorescently labeled plasmids pAB1_FL905 and pAB1_FL924 can be used to study DNA topoisomerase-catalyzed reactions by fluorescence resonance energy transfer (FRET) or supercoiling-dependent fluorescence quenching (SDFQ). With the FRET or SDFQ method, we performed steady-state kinetic studies for six different DNA topoisomerases including two type IA enzymes (Escherichia coli and Mycobacterium smegmatis DNA topoisomerase I), two type IB enzymes (human and variola DNA topoisomerase I), and two type IIA enzymes (E. coli DNA gyrase and human DNA topoisomerase IIα). Our results show that all DNA topoisomerases follow the classical Michaelis-Menten kinetics and have unique steady-state kinetic parameters, K _M, V _max, and k _cat. We found that k _cat for all topoisomerases are rather low and that such low values may stem from the tight binding of topoisomerases to DNA. Additionally, we confirmed that novobiocin is a competitive inhibitor for adenosine 5'-triphosphate binding to E. coli DNA gyrase, demonstrating the utility of our assay for studying topoisomerase inhibitors.

Cu(I) Catalyzed Coumarin-1,2,3-Triazole Hybrids: Click Chemistry

A series of novel coumarin-1,2,3-triazole derivatives were synthesized in good yield via click chemistry using Cu(I) catalyzed intermolecular Huisgen [3+2] cycloaddition reaction. All the synthesized compounds were characterized spectroscopically. This piece of work could be helpful to develop biologically relevant coumarin analogs.

Albicidin, a potent DNA gyrase inhibitor with clinical potential

The emergence of multiple antibiotic-resistant bacteria is a serious global problem which requires the development of new effective antimicrobial therapeutics. Albicidin produced by the sugarcane pathogen Xanthomonas albilineans is a potent DNA gyrase inhibitor with inhibitory effects significantly better than most DNA gyrase inhibitors. Albicidin acts primarily by inhibiting the religation of the cleaved DNA intermediate during the gyrase catalytic sequence similar to quinolones. The clinical realization of albicidin has been hampered by limited production and its unsolved structure. In this review, the relationship between albicidin and sugarcane leaf-scald disease is described. Furthermore, the biosynthesis and resistance mechanisms of albicidin are discussed. Finally, recent efforts to solve the structure and produce albicidin in a heterologous host and chemically are summarized.

A novel molecular scaffold resensitizes multidrug-resistant S. aureus to fluoroquinolones

Nosocomial infections arising from opportunistic pathogens, such as Staphylococcus aureus, are growing unabated, compounded by the rapid emergence of antimicrobial resistance. Herein, we demonstrate a new molecular design that exhibits excellent activity against multidrug-resistant S. aureus with no cytotoxicity and resensitizes fluoroquinolones (FQ) towards FQ-resistant methicillin-resistant S. aureus strains, with DNA gyrase B as the likely molecular target as determined by molecular dynamics (MD) simulations.

Review on plant antimicrobials: a mechanistic viewpoint

Microbial resistance to classical antibiotics and its rapid progression have raised serious concern in the treatment of infectious diseases. Recently, many studies have been directed towards finding promising solutions to overcome these problems. Phytochemicals have exerted potential antibacterial activities against sensitive and resistant pathogens via different mechanisms of action. In this review, we have summarized the main antibiotic resistance mechanisms of bacteria and also discussed how phytochemicals belonging to different chemical classes could reverse the antibiotic resistance. Next to containing direct antimicrobial activities, some of them have exerted in vitro synergistic effects when being combined with conventional antibiotics. Considering these facts, it could be stated that phytochemicals represent a valuable source of bioactive compounds with potent antimicrobial activities.

Identification of new DNA gyrase inhibitors based on bioactive compounds from streptomyces: structure-based virtual screening and molecular dynamics simulations approaches

DNA gyrase enzyme has vital role in bacterial survival and can be considered as a potential drug target. Owing to the appearance of resistance to gyrase-targeted drugs, especially fluoroquinolone, screening new compounds which bind more efficiently to the mutant binding pocket is essential. Hence, in this work, using Smina Autodock and through structure-based virtual screening of StreptomeDB, several natural products were discovered based on the SimocyclinoneD8 (SD8) binding pocket of GyrA subunit of DNA gyrase. After evaluation of binding affinity, binding modes, critical interactions and physicochemical and pharmaceutical properties, three lead compounds were selected for further analysis. Afterward 60 ns molecular dynamics simulations were performed and binding free energies were calculated by the molecular mechanics/Poisson-Boltzmann surface area method. Also, interaction of the selected lead compounds with the mutated GyrA protein was evaluated. Results indicated that all of the selected compounds could bind to the both wild-type and mutated GyrA with the binding affinities remarkably higher than SimocyclinoneD8. Interestingly, we noticed that the selected compounds comprised angucycline moiety in their structure which could sufficiently interact with GyrA and block the DNA binding pocket of DNA gyrase, in silico. In conclusion, three DNA gyrase inhibitors were identified successfully which were highly capable of impeding DNA gyrase and can be considered as potential drug candidates for treatment of fluoroquinolone-resistant strains.Communicated by Ramaswamy H. Sarma.

α-pyrones and their hydroxylated analogs as promising scaffolds against Mycobacterium tuberculosis

Tuberculosis ranks as the leading cause of global human mortality from a single infectious agent. To address the uprising issues of drug resistance, intense research efforts have been directed towards drug discovery. However, it is a long and economically challenging process that is often associated with high failure rates. Therefore, it seems prudent to take forward the core scaffolds that have already acclaimed clinical relevance. In this direction, hydroxylated α-pyrone scaffold has received US FDA approval for human use against HIV. Interestingly, literature review reveals the potential applicability of α-pyrones in TB drug discovery. On one hand, α-pyrones play a vital role in the cell wall of Mycobacterium tuberculosis and on the other hand natural α-pyrones display appreciable anti-TB activity. This review aims to rekindle the interest of researchers toward α-pyrone as a new anti-TB drug that may possibly tackle drug resistance and open a dual frontier in TB and HIV drug discovery.

Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii

Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30 -C40 ) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.

Pharmacophore generation, atom-based 3D-QSAR and molecular dynamics simulation analyses of pyridine-3-carboxamide-6-yl-urea analogues as potential gyrase B inhibitors

DNA gyrase subunit B (GyrB) is an attractive drug target for the development of antibacterial agents with therapeutic potential. In the present study, computational studies based on pharmacophore modelling, atom-based QSAR, molecular docking, free binding energy calculation and dynamics simulation were performed on a series of pyridine-3-carboxamide-6-yl-urea derivatives. A pharmacophore model using 49 molecules revealed structural and chemical features necessary for these molecules to inhibit GyrB. The best fitted model AADDR.13 was generated with a coefficient of determination (r²) of 0.918. This model was validated using test set molecules and had a good r² of 0.78. 3D contour maps generated by the 3D atom-based QSAR revealed the key structural features responsible for the GyrB inhibitory activity. Extra precision molecular docking showed hydrogen bond interactions with key amino acid residues of ATP-binding pocket, important for inhibitor binding. Further, binding free energy was calculated by the MM-GBSA rescoring approach to validate the binding affinity. A 10 ns MD simulation of inhibitor #47 showed the stability of the predicted binding conformations. We identified 10 virtual hits by in silico high-throughput screening. A few new molecules were also designed as potent GyrB inhibitors. The information obtained from these methodologies may be helpful to design novel inhibitors of GyrB.

Targeting quinolone- and aminocoumarin-resistant bacteria with new gyramide analogs that inhibit DNA gyrase

Bacterial DNA gyrase is an essential type II topoisomerase that enables cells to overcome topological barriers encountered during replication, transcription, recombination, and repair. This enzyme is ubiquitous in bacteria and represents an important clinical target for antibacterial therapy. In this paper we report the characterization of three exciting new gyramide analogs-from a library of 183 derivatives-that are potent inhibitors of DNA gyrase and are active against clinical strains of gram-negative bacteria (Escherichia coli, Shigella flexneri, and Salmonella enterica; 3 of 10 wild-type strains tested) and gram-positive bacteria (Bacillus spp., Enterococcus spp., Staphylococcus spp., and Streptococcus spp.; all 9 of the wild-type strains tested). E. coli strains resistant to the DNA gyrase inhibitors ciprofloxacin and novobiocin display very little cross-resistance to these new gyramides. In vitro studies demonstrate that the new analogs are potent inhibitors of the DNA supercoiling activity of DNA gyrase (IC50s of 47-170 nM) but do not alter the enzyme's ATPase activity. Although mutations that confer bacterial cells resistant to these new gyramides map to the genes encoding the subunits of the DNA gyrase (gyrA and gyrB genes), overexpression of GyrA, GyrB, or GyrA and GyrB together does not suppress the inhibitory effect of the gyramides. These observations support the hypothesis that the gyramides inhibit DNA gyrase using a mechanism that is unique from other known inhibitors.

Synthesis, antimicrobial, cytotoxic and E. coli DNA gyrase inhibitory activities of coumarinyl amino alcohols

Here we report the in vitro antimicrobial activity (minimum inhibitory concentration) of fourteen coumarinyl amino alcohols 2-16 against eight bacterial strains and two fungi. Among these compounds 4, 8, 12, 15 and 16 showed moderate to good microbial inhibition with MIC values varied from 6.25 to 25μg/mL. The most promising compounds were also evaluated for their in vitro cytotoxic and E. coli DNA gyrase inhibitory activities along with the two 7-oxy-4-methyl coumarinyl amino alcohol derivatives 17 and 18, which were found to be the most potent in in vitro antimicrobial screening in our previous study. All the active compounds, including 17 and 18, were also docked into the E. coli DNA gyrase ATP binding site (PDB ID: 1KZN) to investigate their binding interactions. Of these compound 17 has shown maximum binding energy value of -6.13kcal/mol.

Receptor-based screening assays for the detection of antibiotics residues - A review

Consumer and regulatory agencies have a high concern to antibiotic residues in food producing animals, so appropriate screening assays of fast, sensitive, low cost, and easy sample preparation for the identification of these residues are essential for the food-safety insurance. Great efforts in the development of a high-throughput antibiotic screening assay have been made in recent years. Concerning the screening of antibiotic residue, this review elaborate an overview on the availability, advancement and applicability of antibiotic receptor based screening assays for the safety assessment of antibiotics usage (i.e. radio receptor assay, enzyme labeling assays, colloidal gold receptor assay, enzyme colorimetry assay and biosensor assay). This manuscript also tries to shed a light on the selection, preparation and future perspective of receptor protein for antibiotic residue detection. These assays have been introduced for the screening of numerous food samples. Receptor based screening technology for antibiotic detection has high accuracy. It has been concluded that at the same time, it can detect a class of drugs for certain receptor, and realize the multi-residue detection. These assays offer fast, easy and precise detection of antibiotics.