scholarly journals Targeting the energy-coupling factor (ECF) transporters: identification of new tool compounds

2021 ◽  
Author(s):  
Eleonora Diamanti ◽  
Inda Setyawati ◽  
Spyridon Bousis ◽  
Paulo C. T. Souza ◽  
leticia mojas ◽  
...  
Keyword(s):  
Energy Coupling ◽  
Coupling Factor ◽  
Coarse Grained ◽  
Design Synthesis ◽  
Screening Design ◽  
Wide Range ◽  
Pharmaceutical Properties ◽  
Vitamin Uptake ◽  
Dynamics Simulations ◽  
Chemical Class

The energy-coupling factor (ECF) transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. Their central role in the metabolism of bacteria and absence in humans make the ECF transporters a potential antibacterial target, which can be further investigated making use of a selective chemical probe. Here, we report on the virtual screening, design, synthesis, structure–activity relationships (SARs) and coarse-grained molecular dynamics simulations of the first class of inhibitors of the ECF transporters. We investigated the mechanism of action of this chemical class and profiled the best hit compounds regarding their pharmaceutical properties. The optimized hit has a minimum inhibitory concentration (MIC) value of 2 µg/mL against Streptococcus pneumoniae, which opens up the possibility to use this chemical class to investigate the role of the ECF transporters in health and disease.

Discovery of Antibacterial Agents Inhibiting the Energy-Coupling Factor (ECF) Transporters by Structure-Based Virtual Screening

2020 ◽  
Author(s):  
Eleonora Diamanti ◽  
Inda Setyawati ◽  
Spyridon Bousis ◽  
leticia mojas ◽  
lotteke Swier ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Antibacterial Agents ◽  
Antimicrobial Agents ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Design Synthesis ◽  
Screening Design ◽  
Starting Point ◽  
Wide Range ◽  
Vitamin Uptake

Here, we report on the virtual screening, design, synthesis and structure–activity relationships (SARs) of the first class of selective, antibacterial agents against the energy-coupling factor (ECF) transporters. The ECF transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. Because of their central role in the metabolism of bacteria and their absence in humans, ECF transporters are novel potential antimicrobial targets to tackle infection. The hit compound’s metabolic and plasma stability, the potency (20, MIC Streptococcus pneumoniae = 2 µg/mL), the absence of cytotoxicity and a lack of resistance development under the conditions tested here suggest that this scaffold may represent a promising starting point for the development of novel antimicrobial agents with an unprecedented mechanism of action.<br>

Discovery of Antibacterial Agents Inhibiting the Energy-Coupling Factor (ECF) Transporters by Structure-Based Virtual Screening

2020 ◽  
Author(s):  
Eleonora Diamanti ◽  
Inda Setyawati ◽  
Spyridon Bousis ◽  
leticia mojas ◽  
lotteke Swier ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Antibacterial Agents ◽  
Antimicrobial Agents ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Design Synthesis ◽  
Screening Design ◽  
Starting Point ◽  
Wide Range ◽  
Vitamin Uptake

Here, we report on the virtual screening, design, synthesis and structure–activity relationships (SARs) of the first class of selective, antibacterial agents against the energy-coupling factor (ECF) transporters. The ECF transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. Because of their central role in the metabolism of bacteria and their absence in humans, ECF transporters are novel potential antimicrobial targets to tackle infection. The hit compound’s metabolic and plasma stability, the potency (20, MIC Streptococcus pneumoniae = 2 µg/mL), the absence of cytotoxicity and a lack of resistance development under the conditions tested here suggest that this scaffold may represent a promising starting point for the development of novel antimicrobial agents with an unprecedented mechanism of action.<br>

scholarly journals Two Essential Arginine Residues in the T Components of Energy-Coupling Factor Transporters

2009 ◽  
Vol 191 (21) ◽  
pp. 6482-6488 ◽  
Author(s):  
Olivia Neubauer ◽  
Anja Alfandega ◽  
Janna Schoknecht ◽  
Ulrich Sternberg ◽  
Anne Pohlmann ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Transmembrane Protein ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Single Mutation ◽  
Modular Assembly ◽  
Double Mutation ◽  
Arginine Residues ◽  
Uptake Activity ◽  
Vitamin Uptake

ABSTRACT Energy-coupling factor (ECF) transporters, a recently discovered class of importers of micronutrients, are composed of a substrate-specific transmembrane component (S component) and a conserved energy-coupling module consisting of a transmembrane protein (T component) and pairs of ABC ATPases (A proteins). Based on utilization of a dedicated (subclass I) or shared (subclass II) energy-coupling module, ECF systems fall into two subclasses. The T components are the least-characterized proteins of ECF importers, and their function is essentially unknown. Using RcBioN and LmEcfT, the T units of the subclass I biotin transporter (RcBioMNY) of a gram-negative bacterium and of the subclass II folate, pantothenate, and riboflavin transporters of a lactic acid bacterium, respectively, we analyzed the role of two strongly conserved short motifs, each containing an arginine residue. Individual replacement of the two Arg residues in RcBioN reduced ATPase activity, an indicator of the transporter function, by two-thirds without affecting the modular assembly of the RcBioMNY complex. A double Arg-to-Glu replacement destroyed the complex and abolished ATPase activity. The corresponding single mutation in motif II of LmEcfT, as well as a double mutation, led to loss of the T unit from the subclass II ECF transporters and inactivated these systems. A single Arg-to-Glu replacement in motif I, however, abolished vitamin uptake activity without affecting assembly of the modules. Our results indicate that the conserved motif I in T components is essential for intramolecular signaling and, in cooperation with motif II, for subunit assembly of modular ECF transporters.

Energy Coupling Factor-Type ABC Transporters for Vitamin Uptake in Prokaryotes

Biochemistry ◽  
2012 ◽  
Vol 51 (22) ◽  
pp. 4390-4396 ◽  
Author(s):  
Guus B. Erkens ◽  
Maria Majsnerowska ◽  
Josy ter Beek ◽  
Dirk Jan Slotboom
Keyword(s):  
Abc Transporters ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Factor Type ◽  
Vitamin Uptake

scholarly journals Membrane fusion and drug delivery with carbon nanotube porins

2021 ◽  
Vol 118 (19) ◽  
pp. e2016974118
Author(s):  
Nga T. Ho ◽  
Marc Siggel ◽  
Karen V. Camacho ◽  
Ramachandra M. Bhaskara ◽  
Jacqueline M. Hicks ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Carbon Nanotube ◽  
Treatment Efficacy ◽  
Lipid Membranes ◽  
Coarse Grained ◽  
Membrane Material ◽  
Cytoplasmic Delivery ◽  
Life Saving ◽  
Wide Range ◽  
Dynamics Simulations

Drug delivery mitigates toxic side effects and poor pharmacokinetics of life-saving therapeutics and enhances treatment efficacy. However, direct cytoplasmic delivery of drugs and vaccines into cells has remained out of reach. We find that liposomes studded with 0.8-nm-wide carbon nanotube porins (CNTPs) function as efficient vehicles for direct cytoplasmic drug delivery by facilitating fusion of lipid membranes and complete mixing of the membrane material and vesicle interior content. Fusion kinetics data and coarse-grained molecular dynamics simulations reveal an unusual mechanism where CNTP dimers tether the vesicles, pull the membranes into proximity, and then fuse their outer and inner leaflets. Liposomes containing CNTPs in their membranes and loaded with an anticancer drug, doxorubicin, were effective in delivering the drug to cancer cells, killing up to 90% of them. Our results open an avenue for designing efficient drug delivery carriers compatible with a wide range of therapeutics.

scholarly journals A Novel Class of Modular Transporters for Vitamins in Prokaryotes

2008 ◽  
Vol 191 (1) ◽  
pp. 42-51 ◽  
Author(s):  
Dmitry A. Rodionov ◽  
Peter Hebbeln ◽  
Aymerick Eudes ◽  
Josy ter Beek ◽  
Irina A. Rodionova ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Transmembrane Protein ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Human Pathogens ◽  
Gram Positive Bacteria ◽  
New Class ◽  
Vitamin Uptake ◽  
Genome Context ◽  
Nucleotide Binding Proteins

ABSTRACT The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have yet to be identified, including the vitamin transporters in various human pathogens, whose growth depends strictly on vitamin uptake. Comparative analysis of the ever-growing collection of microbial genomes coupled with experimental validation enables the discovery of such transporters. Here, we used this approach to discover an abundant class of vitamin transporters in prokaryotes with an unprecedented architecture. These transporters have energy-coupling modules comprised of a conserved transmembrane protein and two nucleotide binding proteins similar to those of ATP binding cassette (ABC) transporters, but unlike ABC transporters, they use small integral membrane proteins to capture specific substrates. We identified 21 families of these substrate capture proteins, each with a different specificity predicted by genome context analyses. Roughly half of the substrate capture proteins (335 cases) have a dedicated energizing module, but in 459 cases distributed among almost 100 gram-positive bacteria, including numerous human pathogens, different and unrelated substrate capture proteins share the same energy-coupling module. The shared use of energy-coupling modules was experimentally confirmed for folate, thiamine, and riboflavin transporters. We propose the name energy-coupling factor transporters for the new class of membrane transporters.

Colloidal Shear Thickening Fluids Using Variable Shaped Functional Star Particles: A Molecular Dynamics Study

2021 ◽  
Author(s):  
Rofiques Salehin ◽  
Rongguang Xu ◽  
Stefanos Papanikolaou
Keyword(s):  
Molecular Dynamics ◽  
Shear Thickening ◽  
Packing Fraction ◽  
Coarse Grained ◽  
Leg Length ◽  
Colloidal Fluids ◽  
Wide Range ◽  
Shear Thickening Fluids ◽  
Functional Complex ◽  
Dynamics Simulations

Complex colloidal fluids, depending on particulates&rsquo; shapes and packing fractions, may have a wide range of shear thinning and thickening behaviors. A particular interesting way to transition between different types of such behavior is by infusing functional complex particles that can be manufactured using modern techicques such as 3D printing. In this paper, we display 2D molecular dynamics simulations of such fluids with infused star-shaped functional particles, with variable leg length and number of legs, as they are infused in a non-interacting, coarse-grained fluid. We vary the packing fraction (ϕ) of the system, and for each different system we apply shear with various strain rate that turns the fluid into a jammed state and rise the apparent viscosity of fluid. We demonstrate the dependence of viscosity with the particles&rsquo; packing fraction. We show the role of shape and design dependence of the functional particles towards the transition to a shear thickening fluid .

scholarly journals Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry

2020 ◽  
Vol 117 (13) ◽  
pp. 7216-7224 ◽  
Author(s):  
Akshay Sridhar ◽  
Stephen E. Farr ◽  
Guillem Portella ◽  
Tamar Schlick ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Large Scale ◽  
Coarse Grained ◽  
Multiscale Approach ◽  
Protein Disorder ◽  
Wide Range ◽  
Chromatin Structural ◽  
Degree Of Condensation ◽  
Dynamics Simulations ◽  
Nucleosome Binding

Protein flexibility and disorder is emerging as a crucial modulator of chromatin structure. Histone tail disorder enables transient binding of different molecules to the nucleosomes, thereby promoting heterogeneous and dynamic internucleosome interactions and making possible recruitment of a wide-range of regulatory and remodeling proteins. On the basis of extensive multiscale modeling we reveal the importance of linker histone H1 protein disorder for chromatin hierarchical looping. Our multiscale approach bridges microsecond-long bias-exchange metadynamics molecular dynamics simulations of atomistic 211-bp nucleosomes with coarse-grained Monte Carlo simulations of 100-nucleosome systems. We show that the long C-terminal domain (CTD) of H1—a ubiquitous nucleosome-binding protein—remains disordered when bound to the nucleosome. Notably, such CTD disorder leads to an asymmetric and dynamical nucleosome conformation that promotes chromatin structural flexibility and establishes long-range hierarchical loops. Furthermore, the degree of condensation and flexibility of H1 can be fine-tuned, explaining chromosomal differences of interphase versus metaphase states that correspond to partial and hyperphosphorylated H1, respectively. This important role of H1 protein disorder in large-scale chromatin organization has a wide range of biological implications.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

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