Isolation of the autoinducer-quenching strain that inhibits LasR in Pseudomonas aeruginosa

A Systematic Hierarchical Virtual Screening Model for RhlR Inhibitors Based on PCA, Pharmacophore, Docking, and Molecular Dynamics

RhlR plays a key role in the quorum sensing of Pseudomonas aeruginosa. The current structure-activity relationship (SAR) studies of RhlR inhibitors mainly focus on elucidating the functional groups. Based on a systematic review of previous research on RhlR inhibitors, this study aims to establish a systematic, hierarchical screening model for RhlR inhibitors. We initially established a database and utilized principal component analysis (PCA) to categorize the inhibitors into two classes. Based on the training set, pharmacophore models were established to elucidate the structural characteristics of ligands. Subsequently, molecular docking, molecular dynamics simulations, and the calculation of binding free energy and strain energy were performed to validate the crucial interactions between ligands and receptors. Then, the screening criteria for RhlR inhibitors were established hierarchically based on ligand structure characteristics, ligand-receptor interaction, and receptor affinity. Test sets were finally employed to validate the hierarchical virtual screening model by comparing it with the current SAR studies of RhlR inhibitors. The hierarchical screening model was confirmed to possess higher accuracy and a true positive rate, which holds promise for subsequent screening and the discovery of active RhlR inhibitors.

Verification and application of a modified carbapenem inactivation method (mCIM) on Pseudomonas aeruginosa: a potential screening methodology on carbapenemases phenotype in Bacillus cereus

Antimicrobial resistance (AMR) has been a leading issue for human health globally threatening the achievement of several of the Sustainable Development Goals (SDGs). Originated from Bacillus cereus, carbapenemases phenotype has been considered to be a major concern in AMR. In this study, the AMR identification rate of P. aeruginosa isolates and infections in FAHJU showed an obvious upward trend from 2012 to 2016. All 88 carbapenem-resistant P. aeruginosa strains were screened for carbapenemase phenotype by modified Carbapenem Inactivation Method (mCIM), and these results of mCIM were compared with traditional PCR results. The isolates of P. aeruginosa and infected patients showed obvious upward trend from 2012 to 2016. The drug resistance to common clinical antibiotics was serious that the clinical rational use of antibiotics should be strengthened, which is in accordance with the Global Antimicrobial Resistance and Use Surveillance System (GLASS) report. In comparison, the results of mCIM showed that 18 out of 88 CRPA strains were carbapenemase positive, which were completely consistent with the results yielded by PCR method. Therefore, it is convinced that this mCIM methodology is a simple and quick method for detected carbapenemases producing P. aeruginosa and has a potential capability in carbapenemases phenotype of pathogen like B. cereus, which will undoubtedly aid in the AMR therapy.

Quorum Sensing Inhibitors: Curbing Pathogenic Infections through Inhibition of Bacterial Communication

Currently, most of the developed and developing countries are facing the problem of infectious diseases. The genius way of an exaggerated application of antibiotics led the infectious agents to respond by bringing a regime of persisters to resist antibiotics attacks prolonging their survival. Persisters have the dexterity to communicate among themself using signal molecules via the process of Quorum Sensing (QS), which regulates virulence gene expression and biofilms formation, making them more vulnerable to antibiotic attack. Our review aims at the different approaches applied in the ordeal to solve the riddle for QS inhibitors. QS inhibitors, their origin, structures and key interactions for QS inhibitory activity have been summarized. Solicitation of a potent QS inhibitor molecule would be beneficial, giving new life to the simplest antibiotics in adjuvant therapy.

In silico Molecular Docking, DFT Analysis and ADMET Studies of Carbazole Alkaloid and Coumarins from Roots of Clausena anisata: A Potent Inhibitor for Quorum Sensing

Introduction

In modern drug design, in silico methods are largely used to understand drug-receptor interactions and quantum chemical properties. In the present study, a computational de novo design approach was used to confirm mode of binding for antibacterial activity, elucidating quantum chemical properties and ADMET-drug-likeness of carbazole alkaloid (1) and three coumarins (2-4) isolated from roots of Clausena anisata.

Methods

Docking studies were performed with DNA-Gyrase (6F86) and LasR binding domain (2UV0) employing a flexible ligand docking approach using AutoDock Vina. SwissADME prediction and toxicological predictions were performed by ADMET. The optimized structures and molecular electrostatic potential surface of the isolated compounds were predicted by DFT analysis using B3LYP/6-31G basis levels.

Results and Discussion

The docking results revealed that compound 3 showed better docking scores against both DNA gyrase B and LasR binding domain compared with ciprofloxacin with potential as an inhibitor of bacterial DNA gyrase and quorum sensing LasR binding domain. The SwissADME prediction results showed that all the isolated compounds (1-4) satisfy Lipinski's rule of five with zero violations. Toxicological prediction results suggested that all compounds and ciprofloxacin are non-hepatotoxic, non-carcinogenic, non-irritant, immunogenic, and non-cytotoxic. The DFT analysis results revealed that compound 3 has large electronegativity (χeV), global softness (σ eV^-1), global electrophilicity (ωeV), and mutagenicity value closer to ciprofloxacin (with LD₅₀ value of 480 mg/kg) suggesting better bioactivity and chemical reactivity with considerable intra-molecular charge transfer between electron-donor to electron-acceptor groups.

Conclusion

Overall, compound 3 may serve as a lead molecule that could be developed into a potent E. coli DNA gyrase B inhibitor and efficient inhibitor for quorum sensing auto-inducer LasR binding domain of Pseudomonas aeruginosa.

5-Episinuleptolide Decreases the Expression of the Extracellular Matrix in Early Biofilm Formation of Multi-Drug Resistant Acinetobacter baumannii

Nosocomial infections and increasing multi-drug resistance caused by Acinetobacter baumannii have been recognized as emerging problems worldwide. Moreover, A. baumannii is able to colonize various abiotic materials and medical devices, making it difficult to eradicate and leading to ventilator-associated pneumonia, and bacteremia. Development of novel molecules that inhibit bacterial biofilm formation may be an alternative prophylactic option for the treatment of biofilm-associated A. baumannii infections. Marine environments, which are unlike their terrestrial counterparts, harbor an abundant biodiversity of marine organisms that produce novel bioactive natural products with pharmaceutical potential. In this study, we identified 5-episinuleptolide, which was isolated from Sinularia leptoclados, as an inhibitor of biofilm formation in ATCC 19606 and three multi-drug resistant A. baumannii strains. In addition, the anti-biofilm activities of 5-episinuleptolide were observed for Gram-negative bacteria but not for Gram-positive bacteria, indicating that the inhibition mechanism of 5-episinuleptolide is effective against only Gram-negative bacteria. The mechanism of biofilm inhibition was demonstrated to correlate to decreased gene expression from the pgaABCD locus, which encodes the extracellular polysaccharide poly-β-(1,6)-N-acetylglucosamine (PNAG). Scanning electron microscopy (SEM) indicated that extracellular matrix of the biofilm was dramatically decreased by treatment with 5-episinuleptolide. Our study showed potentially synergistic activity of combination therapy with 5-episinuleptolide and levofloxacin against biofilm formation and biofilm cells. These data indicate that inhibition of biofilm formation via 5-episinuleptolide may represent another prophylactic option for solving the persistent problem of biofilm-associated A. baumannii infections.

2-Furaldehyde diethyl acetal from tender coconut water (Cocos nucifera) attenuates biofilm formation and quorum sensing-mediated virulence of Chromobacterium violaceum and Pseudomonas aeruginosa

The aim of this study was to evaluate the anti-biofilm and quorum sensing inhibitory (QSI) potential of tender coconut water (TCW) against Chromobacterium violaceum and Pseudomonas aeruginosa. TCW significantly inhibited the QS regulated violacein, virulence factors and biofilm production without affecting their growth. qRT-PCR analysis revealed the down-regulation of autoinducer synthase, transcriptional regulator and virulence genes. Mass-spectrometric analysis of a petroleum ether extract of the TCW hydrolyte revealed that 2-furaldehyde diethyl acetal (2FDA) and palmitic acid (PA) are the major compounds. In vitro bioassays confirmed the ability of 2FDA to inhibit the biofilm formation and virulence factors. In addition, the combination of PA with 2FDA resulted in potent inhibition of biofilm formation and virulence factors. The results obtained strongly suggest that TCW can be exploited as a base for designing a novel antipathogenic drug formulation to treat biofilm mediated infections caused by P. aeruginosa.

Novel approaches to combat bacterial biofilms

Biofilms formed by pathogenic bacteria and fungi are associated with a wide range of diseases, from device-related infections (such as catheters or prosthetic joints) to chronic infections occurring on native tissues (such as lung infections in cystic fibrosis patients). Biofilms are therefore responsible for an important medical and economic burden. Currently used antibiotics have mostly been developed to target exponentially growing microorganisms and are poorly effective against biofilms. In particular, even high concentrations of bactericidal antibiotics are inactive against a subset of persistent biofilm bacteria, which can cause infection recurrence despite prolonged treatments. While the search for a magic bullet antibiotic effective against both planktonic and biofilm bacteria is still active, alternative preventive and curative approaches are currently being developed either limiting adhesion or biofilm formation or targeting biofilm tolerance by killing persister bacteria. Most of these approaches are adjunctive using new molecules in combination with antibiotics. This review presents promising approaches or strategies that could improve our ability to prevent or eradicate bacterial biofilms in medical settings.