Computational modelling of efflux pumps and their inhibitors

2017 ◽  
Vol 61 (1) ◽  
pp. 141-156 ◽  
Author(s):  
Venkata Krishnan Ramaswamy ◽  
Pierpaolo Cacciotto ◽  
Giuliano Malloci ◽  
Attilio V. Vargiu ◽  
Paolo Ruggerone
Keyword(s):  
Rational Design ◽  
Specific Resistance ◽  
Computational Simulation ◽  
Computational Modelling ◽  
Efflux Pumps ◽  
Health Concern ◽  
Gram Negative Bacteria ◽  
Simulation Studies ◽  
Outer Membranes ◽  
Secondary Transporter

Antimicrobial resistance is based on the multifarious strategies that bacteria adopt to face antibiotic therapies, making it a key public health concern of our era. Among these strategies, efflux pumps (EPs) contribute significantly to increase the levels and profiles of resistance by expelling a broad range of unrelated compounds – buying time for the organisms to develop specific resistance. In Gram-negative bacteria, many of these chromosomally encoded transporters form multicomponent ‘pumps’ that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component. One of the strategies to reinvigorate the efficacy of antimicrobials is by joint administration with EP inhibitors (EPI), which either block the substrate binding and/or hinder any of the transport-dependent steps of the pump. In this review, we provide an overview of multidrug-resistance EPs, their inhibition strategies and the relevant findings from the various computational simulation studies reported to date with respect to deciphering the mechanism of action of inhibitors with the purpose of improving their rational design.

scholarly journals Rational Design of an Ion-Imprinted Polymer for Aqueous Methylmercury Sorption

Nanomaterials ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2541
Author(s):  
Ruddy L. M. Mesa ◽  
Javier E. L. Villa ◽  
Sabir Khan ◽  
Rafaella R. Alves Peixoto ◽  
Marcelo A. Morgano ◽  
...  
Keyword(s):  
Density Functional ◽  
Rational Design ◽  
Tap Water ◽  
Computational Simulation ◽  
Health Concern ◽  
Mercury Species ◽  
Ion Imprinted Polymer ◽  
Imprinted Polymer ◽  
Surface Areas ◽  
Ion Imprinted

Methylmercury (MeHg+) is a mercury species that is very toxic for humans, and its monitoring and sorption from environmental samples of water are a public health concern. In this work, a combination of theory and experiment was used to rationally synthesize an ion-imprinted polymer (IIP) with the aim of the extraction of MeHg+ from samples of water. Interactions among MeHg+ and possible reaction components in the pre-polymerization stage were studied by computational simulation using density functional theory. Accordingly, 2-mercaptobenzimidazole (MBI) and 2-mercaptobenzothiazole (MBT), acrylic acid (AA) and ethanol were predicted as excellent sulfhydryl ligands, a functional monomer and porogenic solvent, respectively. Characterization studies by scanning electron microscopy (SEM) and Brunauer–Emmett–Teller (BET) revealed the obtention of porous materials with specific surface areas of 11 m2 g−1 (IIP–MBI–AA) and 5.3 m2 g−1 (IIP–MBT–AA). Under optimized conditions, the maximum adsorption capacities were 157 µg g−1 (for IIP–MBI–AA) and 457 µg g−1 (for IIP–MBT–AA). The IIP–MBT–AA was selected for further experiments and application, and the selectivity coefficients were MeHg+/Hg2+ (0.86), MeHg+/Cd2+ (260), MeHg+/Pb2+ (288) and MeHg+/Zn2+ (1510), highlighting the material’s high affinity for MeHg+. The IIP was successfully applied to the sorption of MeHg+ in river and tap water samples at environmentally relevant concentrations.

scholarly journals An Update on Plant-Derived Compounds as Potential Inhibitors of the Bacterial Efflux Pumps: With Reference to Staphylococcus aureus and Escherichia coli

2018 ◽  
Author(s):  
Saurav Das ◽  
Santosh Kumar ◽  
Pabitra Bhagowati ◽  
Ashish Kumar Singh
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Efflux Pump ◽  
Efflux Pumps ◽  
Health Concern ◽  
Multi Drug Resistance ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
Potential Inhibitors

Bacterial antibiotic resistance has become a major global health concern. One of the main reasons for the development of multi-drug resistance properties in bacteria is due to the bacterial efflux pump systems. They are important transport proteins, mainly involved in the removal of toxic substrates like antibiotics from inner cell environment. These pumps are responsible for the intrinsic ability of bacteria to get resistant to the antibiotic. Various types of efflux pumps are present in the Gram-positive and Gram-negative bacteria. Plant-derived products like Capsaicin, Olympicin A, and Indirubicin were found to be inhibitors of an efflux pump in Staphylococcus aureus similarly Ursolic acid derivatives; Daidzein and Lanatoside C were plant-derived inhibitors of an efflux pump in Escherichia coli. In this review detail information have been provided about efflux pump inhibitors that have been found to be effective in the Gram-positive bacteria and Gram-negative bacteria. The aim of this review is to focus on the role of plant-derived compounds as effective efflux pumps inhibitors with reference to mainly Staphylococcus aureus and Escherichia coli.

Efflux Pumps of Gram-Negative Bacteria, a New Target for New Molecules

2010 ◽  
Vol 999 (999) ◽  
pp. 1-10
Author(s):  
Jean-Marie Pages ◽  
Sandrine Alibert-Franco ◽  
Abdallah Mahamoud ◽  
Jean-Michel Bolla ◽  
Anne Davin-Regli ◽  
...  
Keyword(s):  
Efflux Pumps ◽  
Gram Negative Bacteria ◽  
Gram Negative

scholarly journals A Simple Method for Assessment of MDR Bacteria for Over-Expressed Efflux Pumps

2013 ◽  
Vol 7 (1) ◽  
pp. 72-82 ◽  
Author(s):  
Marta Martins ◽  
Matthew P McCusker ◽  
Miguel Viveiros ◽  
Isabel Couto ◽  
Séamus Fanning ◽  
...  
Keyword(s):  
Ethidium Bromide ◽  
Efflux Pump ◽  
Efflux Pumps ◽  
Outer Cell ◽  
Gram Negative Bacteria ◽  
Drug Resistant ◽  
Topoisomerase Iv ◽  
Simple Method ◽  
Gram Negative ◽  
Over Expression

It is known that bacteria showing a multi-drug resistance phenotype use several mechanisms to overcome the action of antibiotics. As a result, this phenotype can be a result of several mechanisms or a combination of thereof. The main mechanisms of antibiotic resistance are: mutations in target genes (such as DNA gyrase and topoisomerase IV); over-expression of efflux pumps; changes in the cell envelope; down regulation of membrane porins, and modified lipopolysaccharide component of the outer cell membrane (in the case of Gram-negative bacteria). In addition, adaptation to the environment, such as quorum sensing and biofilm formation can also contribute to bacterial persistence. Due to the rapid emergence and spread of bacterial isolates showing resistance to several classes of antibiotics, methods that can rapidly and efficiently identify isolates whose resistance is due to active efflux have been developed. However, there is still a need for faster and more accurate methodologies. Conventional methods that evaluate bacterial efflux pump activity in liquid systems are available. However, these methods usually use common efflux pump substrates, such as ethidium bromide or radioactive antibiotics and therefore, require specialized instrumentation, which is not available in all laboratories. In this review, we will report the results obtained with the Ethidium Bromide-agar Cartwheel method. This is an easy, instrument-free, agar based method that has been modified to afford the simultaneous evaluation of as many as twelve bacterial strains. Due to its simplicity it can be applied to large collections of bacteria to rapidly screen for multi-drug resistant isolates that show an over-expression of their efflux systems. The principle of the method is simple and relies on the ability of the bacteria to expel a fluorescent molecule that is substrate for most efflux pumps, ethidium bromide. In this approach, the higher the concentration of ethidium bromide required to produce fluorescence of the bacterial mass, the greater the efflux capacity of the bacterial cells. We have tested and applied this method to a large number of Gram-positive and Gram-negative bacteria to detect efflux activity among these multi-drug resistant isolates. The presumptive efflux activity detected by the Ethidium Bromide-agar Cartwheel method was subsequently confirmed by the determination of the minimum inhibitory concentration for several antibiotics in the presence and absence of known efflux pump inhibitors.

scholarly journals Rational Design of Ag/ZnO Hybrid Nanoparticles on Sericin/Agarose Composite Film for Enhanced Antimicrobial Applications

2020 ◽  
Vol 22 (1) ◽  
pp. 105
Author(s):  
Wanting Li ◽  
Zixuan Huang ◽  
Rui Cai ◽  
Wan Yang ◽  
Huawei He ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Antimicrobial Activity ◽  
Composite Film ◽  
Water Absorption ◽  
Rational Design ◽  
Hybrid Nanoparticles ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
X Ray

Silver-based hybrid nanomaterials are receiving increasing attention as potential alternatives for traditional antimicrobial agents. Here, we proposed a simple and eco-friendly strategy to efficiently assemble zinc oxide nanoparticles (ZnO) and silver nanoparticles (AgNPs) on sericin-agarose composite film to impart superior antimicrobial activity. Based on a layer-by-layer self-assembly strategy, AgNPs and ZnO were immobilized on sericin-agarose films using the adhesion property of polydopamine. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray powder diffraction spectroscopy were used to show the morphology of AgNPs and ZnO on the surface of the composite film and analyze the composition and structure of AgNPs and ZnO, respectively. Water contact angle, swelling ratio, and mechanical property were determined to characterize the hydrophilicity, water absorption ability, and mechanical properties of the composite films. In addition, the antibacterial activity of the composite film was evaluated against Gram-positive and Gram-negative bacteria. The results showed that the composite film not only has desirable hydrophilicity, high water absorption ability, and favorable mechanical properties but also exhibits excellent antimicrobial activity against both Gram-positive and Gram-negative bacteria. It has shown great potential as a novel antimicrobial biomaterial for wound dressing, artificial skin, and tissue engineering.

scholarly journals Super-Cationic Peptide Dendrimers—Synthesis and Evaluation as Antimicrobial Agents

Antibiotics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 695
Author(s):  
Estelle J. Ramchuran ◽  
Isabel Pérez-Guillén ◽  
Linda A. Bester ◽  
René Khan ◽  
Fernando Albericio ◽  
...  
Keyword(s):  
Antibacterial Agent ◽  
Antimicrobial Agents ◽  
Health Concern ◽  
Gram Negative Bacteria ◽  
Cationic Peptide ◽  
Public Health Concern ◽  
Gram Negative ◽  
Peptide Dendrimers ◽  
Microbial Infections ◽  
Lead Candidate

Microbial infections are a major public health concern. Antimicrobial peptides (AMPs) have been demonstrated to be a plausible alternative to the current arsenal of drugs that has become inefficient due to multidrug resistance. Herein we describe a new AMP family, namely the super-cationic peptide dendrimers (SCPDs). Although all members of the series exert some antibacterial activity, we propose that special attention should be given to (KLK)2KLLKLL-NH2 (G1KLK-L2KL2), which shows selectivity for Gram-negative bacteria and virtually no cytotoxicity in HepG2 and HEK293. These results reinforce the validity of the SCPD family as a valuable class of AMP and support G1KLK-L2KL2 as a strong lead candidate for the future development of an antibacterial agent against Gram-negative bacteria.

Characterization of lipopolysaccharide transport protein complex

2014 ◽  
Vol 9 (2) ◽  
pp. 131-138
Author(s):  
Quanju Xiang ◽  
Haiyan Wang ◽  
Zhongshan Wang ◽  
Yizheng Zhang ◽  
Changjiang Dong
Keyword(s):  
Transport Mechanism ◽  
Transport Proteins ◽  
Gram Negative Bacteria ◽  
Inner Membrane ◽  
Toxic Compounds ◽  
Outer Membranes ◽  
Harsh Conditions ◽  
Cytoplasmic Side

AbstractLipopolysaccharide (LPS) is an essential component of the outer membranes (OM) of most Gram-negative bacteria, which plays a crucial role in protection of the bacteria from toxic compounds and harsh conditions. The LPS is biosynthesized at the cytoplasmic side of inner membrane (IM), and then transported across the aqueous periplasmic compartment and assembled correctly at the outer membrane. This process is accomplished by seven LPS transport proteins (LptA-G), but the transport mechanism remains poorly understood. Here, we present findings by pull down assays in which the periplasmic component LptA interacts with both the IM complex LptBFGC and the OM complex LptDE in vitro, but not with complex LptBFG. Using purified Lpt proteins, we have successfully reconstituted the seven transport proteins as a complex in vitro. In addition, the LptC may play an essential role in regulating the conformation of LptBFG to secure the lipopolysaccharide from the inner membrane. Our results contribute to the understanding of lipopolysaccharide transport mechanism and will provide a platform to study the detailed mechanism of the LPS transport in vitro.

scholarly journals Tumor-Intrinsic Mechanisms Regulating Immune Exclusion in Liver Cancers

2021 ◽  
Vol 12 ◽  
Author(s):  
Katherine E. Lindblad ◽  
Marina Ruiz de Galarreta ◽  
Amaia Lujambio
Keyword(s):  
Liver Cancer ◽  
Rational Design ◽  
Immune Escape ◽  
Current Knowledge ◽  
Treatment Options ◽  
Health Concern ◽  
Patient Stratification ◽  
Tumor Immune Evasion ◽  
Advanced Hcc ◽  
Liver Cancers

Representing the fourth leading cause of cancer-related mortality worldwide, liver cancers constitute a major global health concern. Hepatocellular carcinoma (HCC), the most frequent type of liver cancer, is associated with dismal survival outcomes and has traditionally had few treatment options available. In fact, up until 2017, treatment options for advanced HCC were restricted to broad acting tyrosine kinase inhibitors, including Sorafenib, which has been the standard of care for over a decade. Since 2017, a multitude of mono- and combination immunotherapies that include pembrolizumab, nivolumab, ipilumumab, atezolizumab, and bevacizumab have been FDA-approved for the treatment of advanced HCC with unprecedented response rates ranging from 20 to 30% of patients. However, this also means that ~70% of patients do not respond to this treatment and currently very little is known regarding mechanisms of action of these immunotherapies as well as predictors of response to facilitate patient stratification. With the recent success of immunotherapies in HCC, there is a pressing need to understand mechanisms of tumor immune evasion and resistance to these immunotherapies in order to identify biomarkers of resistance or response. This will enable better patient stratification as well as the rational design of combination immunotherapies to restore sensitivity in resistant patients. The aim of this review is to summarize the current knowledge to date of tumor-intrinsic mechanisms of immune escape in liver cancer, specifically in the context of HCC.

scholarly journals Antibiotic transport kinetics in Gram-negative bacteria revealed via single-cell uptake analysis and mathematical modelling

2019 ◽  
Author(s):  
Jehangir Cama ◽  
Margaritis Voliotis ◽  
Jeremy Metz ◽  
Ashley Smith ◽  
Jari Iannucci ◽  
...  
Keyword(s):  
Rational Design ◽  
Cell Envelope ◽  
Time Lapse ◽  
Drug Accumulation ◽  
Cell Uptake ◽  
Gram Negative Bacteria ◽  
Label Free ◽  
Transport Pathways ◽  
Gram Negative ◽  
Accumulation Kinetics

AbstractThe double-membrane cell envelope of Gram-negative bacteria is a formidable barrier to intracellular antibiotic accumulation. A quantitative understanding of antibiotic transport in these cells is crucial for drug development, but this has proved elusive due to the complexity of the problem and a dearth of suitable investigative techniques. Here we combine microfluidics and time-lapse auto-fluorescence microscopy to quantify antibiotic uptake label-free in hundreds of individual Escherichia coli cells. By manipulating the microenvironment, we showed that drug (ofloxacin) accumulation is higher in growing versus non-growing cells. Using genetic knockouts, we provide the first direct evidence that growth phase is more important for drug accumulation than the presence or absence of individual transport pathways. We use our experimental results to inform a mathematical model that predicts drug accumulation kinetics in subcellular compartments. These novel experimental and theoretical results pave the way for the rational design of new Gram-negative antibiotics.

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