Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review

Hevea brasiliensis rubber particles' fluid interfaces reveal size impact on early coagulation steps

Natural rubber originates from the coagulation of rubber particles (RP) from Hevea brasiliensis latex. The size distribution of Hevea RP is bimodal with the presence of small rubber particles (SRP) and large rubber particles (LRP). This study aims at getting a better understanding of the early coagulation steps of Hevea RP taking into account the particle size. SRP and LRP were obtained by centrifugation of freshly tapped ammonia-free latex from RRIM600 clone. Size and zeta potential measurements showed that both RP fractions were efficiently separated and stable in basic buffer. SRP and LRP dispersions were placed in a Langmuir trough and RP were let to adsorb at the air-liquid interface to form interfacial films. Surface tension and ellipsometry indicate that the formation kinetics and the stabilization of the film at the air-liquid interface are faster for SRP than LRP. Moreover, the arrangement of RP at the interface differs between SRP and LRP, as shown by Brewster angle microscopy, atomic force microscopy and confocal laser scanning microscopy. First, the RP membrane and cis-1,4-polyisoprene core spread at the air-liquid interface before clustering. Then, while the SRP fuse, the LRP keep their structure in individual particles in floating aggregate. The role of the non-isoprene molecules on the different organization of SRP and LRP films is discussed, the one of the two major RP proteins, SRPP1 (Small Rubber Particle Protein) and Rubber Elongation Factor (REF1) in the early coagulation steps.

Time-resolved fluorescence of tryptophan characterizes membrane perturbation by cyclic lipopeptides

Viscosin is a membrane-permeabilizing, cyclic lipopeptide (CLiP) produced by Pseudomonas species. Here, we have studied four synthetic analogs (L1W, V4W, L5W, and L7W), each with one leucine (Leu; L) or valine residue exchanged for tryptophan (Trp; W) by means of time-resolved fluorescence spectroscopy of Trp. To this end, we recorded the average fluorescence lifetime, rotational correlation time and limiting anisotropy, dipolar relaxation time and limiting extent of relaxation, rate constant of acrylamide quenching, effect of H2O-D2O exchange, and time-resolved half-width of the spectrum in the absence and presence of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) liposomes. Structure, localization, and hydration of the peptides were described by molecular dynamics simulations. The combination of the parameters provides a good description of the molecular environments of the Trp positions and the behavior of viscosin as a whole. Of particular value for characterizing the impact of viscosin on the membrane is the dipolar relaxation of Trp4 in V4W, which is deeply embedded in the hydrophobic core. The limiting relaxation level represents the membrane perturbation-unlike typical membrane probes-at the site of the perturbant. Fractions of Trp4 relax at different rates; the one not in contact with water upon excitation relaxes via recruitment of a water molecule on the 10-ns timescale. This rate is sensitive to the concerted membrane perturbation by more than one lipopeptide, which appears at high lipopeptide concentration and is assumed a prerequisite for the final formation of a membrane-permeabilizing defect. Trp7 relaxes primarily with respect to neighboring Ser residues. Trp5 flips between a membrane-inserted and surface-exposed orientation.

Studies of Protein Binding to Biomimetic Membranes Using a Group of Uniform Materials Based on Organic Salts Derived From 8-Anilino-1-naphthalenesulfonic Acid

Tuning the 8-anilino-1-naphthalenesulfonic acid (ANS) structure usually requires harsh conditions and long reaction times, which can result in low yields. Herein, ANS was modified to form an ANS group of uniform materials based on organic salts (GUMBOS), prepared with simple metathesis reactions and distinct cations, namely tetrabutylammonium (N4444), tetrahexylammonium (N6666), and tetrabutylphosphonium (P4444). These ANS-based GUMBOS were investigated as fluorescent probes for membrane binding studies with four proteins having distinct physicochemical properties. Liposomes of 1,2-dimyristoyl-sn-glycero-3-phosphocholine were employed as membrane models as a result of their ability to mimic the structure and chemical composition of cell membranes. Changes in fluorescence intensity were used to monitor protein binding to liposomes, and adsorption data were fitted to a Freundlich-like isotherm. It was determined that [N4444][ANS] and [P4444][ANS] GUMBOS have enhanced optical properties and lipophilicity as compared to parent ANS. As a result, these two GUMBOS were selected for subsequent protein-membrane binding studies. Both [N4444][ANS] and [P4444][ANS] GUMBOS and parent ANS independently reached membrane saturation within the same concentration range. Furthermore, distinct fluorescence responses were observed upon the addition of proteins to each probe, which demonstrates the impact of properties such as lipophilicity on the binding process. The relative maintenance of binding cooperativity and maximum fluorescence intensity suggests that proteins compete with ANS-based probes for the same membrane binding sites. Finally, this GUMBOS-based approach is simple, rapid, and involves relatively small amounts of reagents, making it attractive for high-throughput purposes. These results presented herein can also provide relevant information for designing GUMBOS with ameliorated properties.

Deciphering the distinct biocontrol activities of lipopeptides fengycin and surfactin through their differential impact on lipid membranes

Lipopeptides produced by beneficial bacilli present promising alternatives to chemical pesticides for plant biocontrol purposes. Our research explores the distinct plant biocontrol activities of lipopeptides surfactin (SRF) and fengycin (FGC) by examining their interactions with lipid membranes. Our study shows that FGC exhibits a direct antagonistic activity against Botrytis cinerea and no marked immune-eliciting activity in Arabidopsis thaliana while SRF only demonstrates an ability to stimulate plant immunity. It also reveals that SRF and FGC exhibit diverse effects on membrane integrity and lipid packing. SRF primarily influences membrane physical state without significant membrane permeabilization, while FGC permeabilizes membranes without significantly affecting lipid packing. From our results, we can suggest that the direct antagonistic activity of lipopeptides is linked to their capacity to permeabilize lipid membrane while the stimulation of plant immunity is more likely the result of their ability to alter the mechanical properties of the membrane. Our work also explores how membrane lipid composition modulates the activities of SRF and FGC. Sterols negatively impact both lipopeptides' activities while sphingolipids mitigate the effects on membrane lipid packing but enhance membrane leakage. In conclusion, our findings emphasize the importance of considering both membrane lipid packing and leakage mechanisms in predicting the biological effects of lipopeptides. It also sheds light on the intricate interplay between the membrane composition and the effectiveness of the lipopeptides, providing insights for targeted biocontrol agent design.

Molecular interactions with bilayer membrane stacks using neutron and X-ray diffraction

Lamellar unit cell reconstruction from neutron and X-ray diffraction data provides information about the disposition and position of molecules and molecular segments with respect to the bilayer. When supplemented with the judicious use of molecular deuteration, the technique probes the molecular interactions and conformations within the bilayer membrane and the water layer which constitute the crystallographic unit cell. The perspective is model independent, and potentially, with a higher degree of resolution than is available with other techniques. In the case of neutron diffraction the measurement consists of carefully normalised diffracted intensity under conditions of contrast variation of the water layer. The subsequent Fourier reconstruction of the unit cell is made using the phase information from variation of peak intensities with contrast. Although the phase problem is not as easily solved for the corresponding X-ray measurements, an intuitive approach can often suffice. Here we discuss the two complimentary techniques as probes of scattering length density profiles of a bilayer, and how such a perspective provides information about the location and orientation of molecules within or between lipid bilayers. Within the basic paradigm of lamellar phases this method has provided, for example, detailed insights into the location and interaction of cryoprotectants and stress proteins, of the mechanisms of actions of viral proteins, antimicrobial compounds and drugs, and the underlying structure of the stratum corneum. In this paper we review these techniques and provide examples of the systems that have been examined. We finish with a future outlook on the use of these techniques to improve our understanding of the interactions of membranes with biomolecules.

Insights into the Adsorption Mechanisms of the Antimicrobial Peptide CIDEM-501 on Membrane Models

CIDEM-501 is a hybrid antimicrobial peptide rationally designed based on the structure of panusin and panulirin template peptides. The new peptide exhibits significant antibacterial activity against multidrug-resistant pathogens (MIC = 2-4 μM) while conserving no toxicity in human cell lines. We conducted molecular dynamics (MD) simulations using the CHARMM-36 force field to explore the CIDEM-501 adsorption mechanism with different membrane compositions. Several parameters that characterize these interactions were analyzed to elucidate individual residues' structural and thermodynamic contributions. The membrane models were constructed using CHARMM-GUI, mimicking the bacterial and eukaryotic phospholipid compositions. Molecular dynamics simulations were conducted over 500 ns, showing rapid and highly stable peptide adsorption to bacterial lipids components rather than the zwitterionic eucaryotic model membrane. A predominant peptide orientation was observed in all models dominated by an electric dipole. The peptide remained parallel to the membrane surface with the center loop oriented to the lipids. Our findings shed light on the antibacterial activity of CIDEM-501 on bacterial membranes and yield insights valuable for designing potent antimicrobial peptides targeting multi- and extreme drug-resistant bacteria.

The Designed Pore-Forming Antimicrobial Peptide C14R Combines Excellent Activity against the Major Opportunistic Human Pathogen Pseudomonas aeruginosa with Low Cytotoxicity

The diminishing portfolio of mankind's available antibiotics urges science to develop novel potent drugs. Here, we present a peptide fitting the typical blueprint of amphipathic and membrane-active antimicrobial peptides, denominated C14R. This 2 kDa peptide consists of 16 amino acid residues, with seven being either hydrophobic, aromatic, or non-polar, and nine being polar or positively charged, strictly separated on opposite sides of the predicted α-helix. The affinity of the peptide C14R to P. aeruginosa membranes and its intrinsic tendency to productively insert into membranes of such composition were analyzed by dynamic simulations. Its biological impact on the viability of two different P. aeruginosa reference strains was demonstrated by determining the minimal inhibitory concentrations (MICs), which were found to be in the range of 10-15 µg/mL. C14R's pore-forming capability was verified in a permeabilization assay based on the peptide-triggered uptake of fluorescent dyes into the bacterial cells. Finally, the peptide was used in radial diffusion assays, which are commonly used for susceptibility testing of antimicrobial peptides in clinical microbiology. In comparison to reference strains, six clinical P. aeruginosa isolates were clearly affected, thereby paving the way for further in-depth analyses of C14R as a promising new AMP drug in the future.

The Structure of Oxysterols Determines Their Behavior at Phase Boundaries: Implications for Model Membranes and Structure-Activity Relationships

The presence of an additional polar group in the cholesterol backbone increases the hydrophilicity of resulting compounds (oxysterols), determines their arrangement at the phase boundary, and interactions with other lipids and proteins. As a result, physicochemical properties of biomembranes (i.e., elasticity, permeability, and ability to bind proteins) are modified, which in turn may affect their functioning. The observed effect depends on the type of oxysterol and its concentration and can be both positive (e.g., antiviral activity) or negative (disturbance of cholesterol homeostasis, signal transduction, and protein segregation). The membrane activity of oxysterols has been successfully studied using membrane models (vesicles, monolayers, and solid supported films). Membrane models, in contrast to the natural systems, provide the possibility to selectively examine the specific aspect of biomolecule-membrane interactions. Moreover, the gradual increase in the complexity of the used model allows to understand the molecular phenomena occurring at the membrane level. The interest in research on artificial membranes has increased significantly in recent years, mainly due to the development of modern and sophisticated physicochemical methods (static and dynamic) in both the micro- and nanoscale, which are applied with the assistance of powerful theoretical calculations. This review provides an overview of the most important findings on this topic in the current literature.

Mimicking effects of cholesterol in lipid bilayer membranes by self-assembled amphiphilic block copolymers

The effect of cholesterol on biological membranes is important in biochemistry. In this study, a polymer system is used to simulate the consequences of varying cholesterol content in membranes. The system consists of an AB-diblock copolymer, a hydrophilic homopolymer hA, and a hydrophobic rigid homopolymer C, corresponding to phospholipid, water, and cholesterol, respectively. The effect of the C-polymer content on the membrane is studied within the framework of a self-consistent field model. The results show that the liquid-crystal behavior of B and C has a great influence on the chemical potential of cholesterol in bilayer membranes. The effects of the interaction strength between components, characterized by the Flory-Huggins parameters and the Maier-Saupe parameter, were studied. Some consequences of adding a coil headgroup to the C-rod are presented. Results of our model are compared to experimental findings for cholesterol-containing lipid bilayer membranes.

Influence of DUX4 Expression in Facioscapulohumeral Muscular Dystrophy and Possible Treatments

Facioscapulohumeral muscular dystrophy (FSHD) represents the third most common form of muscular dystrophy and is characterized by muscle weakness and atrophy. FSHD is caused by the altered expression of the transcription factor double homeobox 4 (DUX4), which is involved in several significantly altered pathways required for myogenesis and muscle regeneration. While DUX4 is normally silenced in the majority of somatic tissues in healthy individuals, its epigenetic de-repression has been linked to FSHD, resulting in DUX4 aberrant expression and cytotoxicity in skeletal muscle cells. Understanding how DUX4 is regulated and functions could provide useful information not only to further understand FSHD pathogenesis, but also to develop therapeutic approaches for this disorder. Therefore, this review discusses the role of DUX4 in FSHD by examining the possible molecular mechanisms underlying the disease as well as novel pharmacological strategies targeting DUX4 aberrant expression.

Regulation of calcium ions on the interaction between amphotericin B and cholesterol-rich phospholipid monolayer in LE phase and LC phase

Amphotericin B, as a "gold standard", is used to treat invasive fungal infections. The AmB molecule can bind easily to cholesterol and damage cell membranes, so it produces the toxicity on cell membrane, which limits its clinical dose. However, the interaction between AmB and cholesterol-rich membrane is unclear now. The phase state of the membrane and the metal cation outside cell membrane may affect the interaction between AmB and the membrane. In this work, the effects of amphotericin B on the mean molecular area, elastic modulus and stability of mammalian cell membrane rich in cholesterol in the presence of Ca²⁺ ions were studied using DPPC/Chol mixed Langmuir monolayer as a model. The Langmuir-Blodgett method and AFM test were used to study the effects of this drug on the morphology and height of cholesterol-rich phospholipid membrane in the presence of Ca²⁺ ions. The influence of calcium ions on the mean molecular area and the limiting molecular area was similar in LE phase and in LC phase. The calcium ions made the monolayer more condensed. However, calcium ions can weaken the shortening effect of AmB on the relaxation time of the DPPC/Chol mixed monolayer in LE phase but enhance it in LC phase. Interestingly, calcium ions caused a LE-LC coexistence phase to occur in the DPPC/Chol/AmB mixed monolayers at 35mN/m, which was confirmed by atomic force microscopy. The results can help to understand the interaction between amphotericin B and cell membrane rich in cholesterol in the calcium ions environment.

Effect of Anionic Lipids on Mammalian Plasma Cell Membrane Properties

The effect of lipid composition on models of the inner leaflet of mammalian cell membranes has been investigated. Grazing incidence X-ray diffraction and X-ray and neutron reflectivity have been used to characterize lipid packing and solvation, while electrochemical and infrared spectroscopic methods have been employed to probe phase behavior in an applied electric field. Introducing a small quantity of the anionic lipid dimyristoylphosphatidylserine (DMPS) into bilayers of zwitterionic dimyristoylphosphatidylethanolamine (DMPE) results in a significant change in the bilayer response to an applied field: the tilt of the hydrocarbon chains increases before returning to the original tilt angle on detachment of the bilayer. Equimolar mixtures, with slightly closer chain packing, exhibit a similar but weaker response. The latter also tend to incorporate more solvent during this electrochemical phase transition, at levels similar to those of pure DMPS. Reflectivity measurements reveal greater solvation of lipid layers for DMPS > 30 mol %, matching the greater propensity for DMPS-rich bilayers to incorporate water. Taken together, the data indicate that the range of 10-35 mol % DMPS provides optimum bilayer properties (in flexibility and function as a barrier), which may explain why the DMPS content of cell membranes tends to be found within this range.

Effects of Natural Rhamnolipid Mixture on Dioleoylphosphatidylcholine Model Membrane Depending on Method of Preparation and Sterol Content

Rhamnolipids as biosurfactants have a potentially wide range of applications, for example, as "green" surfactants or components of drug delivery systems, which is associated with the features of their interaction with cell membranes. However, as noted in the literature, those kind of features have not been sufficiently studied now. This paper presents a study of the interaction of a natural mixture of rhamnolipids produced by bacteria of the rhizosphere zone of plants Pseudomonas aeruginosa with model membranes-liposomes based on dioleoylphosphatidylcholine (DOPC), depending on the method of their preparation and the content of sterols-ergosterol, cholesterol, lanosterol. Liposomes with rhamnolipids were prepared by two protocols: with film method from a mixture of DOPC and rhamnolipids; with film method from DOPC and injection of water solution of rhamnolipids. Joint analysis of the data of 31P NMR spectroscopy and ATR-FTIR spectroscopy showed that in the presence of rhamnolipids, the mobility of the head group of the DOPC phospholipid increases, the conformational disorder of the hydrophobic tail increases, and the degree of hydration of the C=O and P=O groups of the phospholipid decreases. It can be assumed that, when prepared from a mixture, rhamnolipids are incorporated into the membrane in the form of clusters and are located closer to the middle of the bilayer; while when prepared by injection, rhamnolipid molecules migrate into the membrane in the form of individual molecules and are located closer to the head part of phospholipids. The sterol composition of the model membrane also affects the interaction of rhamnolipids with the membrane. Here it is worth noting the possible presence of type of interaction between rhamnolipids and ergosterol differ from other investigated sterols, due to which rhamnolipid molecules are embedded in the area where ergosterol is located.

Effect of Local Stress on Accurate Modeling of Bacterial Outer Membranes Using All-Atom Molecular Dynamics

Biological membranes are fundamental components of living organisms that play an undeniable role in their survival. Molecular dynamics (MD) serves as an essential computational tool for studying biomembranes on molecular and atomistic scales. The status quo of MD simulations of biomembranes studies a nanometer-sized membrane patch periodically extended under periodic boundary conditions (PBCs). In nature, membranes are usually composed of different lipids in their two layers (referred to as leaflets). This compositional asymmetry imposes a fixed ratio of lipid numbers between the two leaflets in a periodically constrained membrane, which needs to be set appropriately. The widely adopted methods of defining a leaflet lipid ratio suffer from the lack of control over the mechanical tension of each leaflet, which could significantly influence research findings. In this study, we investigate the role of membrane-building protocol and the resulting initial stress state on the interaction between small molecules and asymmetric membranes. We model the outer membrane of Pseudomonas aeruginosa bacteria using two different building protocols and probe their interactions with the Pseudomonas quinolone signal (PQS). Our results show that differential stress could shift the position of free energy minimum for the PQS molecule between the two leaflets of the asymmetric membrane. This work provides critical insights into the relationship between the initial per-leaflet tension and the spontaneous intercalation of PQS.

The effect of rhamnolipids on fungal membrane models as described by their interactions with phospholipids and sterols: An in silico study

Introduction: Rhamnolipids (RLs) are secondary metabolites naturally produced by bacteria of the genera Pseudomonas and Burkholderia with biosurfactant properties. A specific interest raised from their potential as biocontrol agents for crop culture protection in regard to direct antifungal and elicitor activities. As for other amphiphilic compounds, a direct interaction with membrane lipids has been suggested as the key feature for the perception and subsequent activity of RLs. Methods: Molecular Dynamics (MD) simulations are used in this work to provide an atomistic description of their interactions with different membranous lipids and focusing on their antifungal properties. Results and discussion: Our results suggest the insertion of RLs into the modelled bilayers just below the plane drawn by lipid phosphate groups, a placement that is effective in promoting significant membrane fluidification of the hydrophobic core. This localization is promoted by the formation of ionic bonds between the carboxylate group of RLs and the amino group of the phosphatidylethanolamine (PE) or phosphatidylserine (PS) headgroups. Moreover, RL acyl chains adhere to the ergosterol structure, forming a significantly higher number of van der Waals contact with respect to what is observed for phospholipid acyl chains. All these interactions might be essential for the membranotropic-driven biological actions of RLs.

Structural Flexibility of Proteins Dramatically Alters Membrane Stability─A Novel Aspect of Lipid-Protein Interaction

Protein isoforms are structural variants with changes in the overall flexibility predominantly at the tertiary level. For membrane associated proteins, such structural flexibility or rigidity affects membrane stability by playing modulatory roles in lipid-protein interaction. Herein, we investigate the protein chain flexibility mediated changes in the mechanistic behavior of phospholipid model membranes in the presence of two well-known isoforms, erythroid (ER) and nonerythroid (NER) spectrin. We show dramatic alterations of membrane elasticity and stability induced by spectrin in the Langmuir monolayers of phosphatidylocholine (PC) and phosphatidylethanolamine (PE) by a combination of isobaric relaxation, surface pressure-area isotherm, X-ray scattering, and microscopy measurements. The NER spectrin drives all monolayers to possess an approximately equal stability, and that required 25-fold increase and 5-fold decrease of stability in PC and PE monolayers, respectively. The untilting transition of the PC membrane in the presence of NER spectrin observed in X-ray measurements can explain better membrane packing and stability.

NMR Studies on the Interaction of Anticancer Drug Doxorubicin with Membrane Mimetic SDS

In the formulation of efficient drug delivery systems, it is essential to unravel the structural and dynamical aspects of the drug's interaction with biological membranes. This has been done for the anticancer drug-membrane system comprising doxorubicin hydrochloride (DOX), a water-soluble anticancer drug, and the micellar sodium dodecyl sulfate (SDS), the latter serving as a useful mimic for membrane proteins. Using a multimodal NMR approach involving ¹H, ²H, and ¹³C as probe nuclei and through the determination of chemical shifts, spin-relaxation, nuclear Overhauser enhancements (NOE), and translational self-diffusion (SD), the binding characteristics of the DOX with SDS have been determined. The perturbation to ¹³C chemical shifts of SDS indicate the penetration of DOX into the SDS micelle, which is further revealed by ¹H-¹H NOESY and SD measurements. ²H spin-relaxation measurements and their analysis using a two-step model show DOX induced SDS micellar volume changes, which determine the correlation times involved in the DOX-SDS mobility.

Encapsulation of Vitamin C by Glycerol-Derived Dendrimers, Their Interaction with Biomimetic Models of Stratum corneum and Their Cytotoxicity

Vitamin C is one of the most sensitive cosmetic active ingredients. To avoid its degradation, its encapsulation into biobased carriers such as dendrimers is one alternative of interest. In this work, we wanted to evaluate the potential of two biobased glycerodendrimer families (GlyceroDendrimers-Poly(AmidoAmine) (GD-PAMAMs) or GlyceroDendrimers-Poly(Propylene Imine) (GD-PPIs)) as a vitamin C carrier for topical application. The higher encapsulation capacity of GD-PAMAM-3 compared to commercial PAMAM-3 and different GD-PPIs, and its absence of cytotoxicity towards dermal cells, make it a good candidate. Investigation of its mechanism of action was done by using two kinds of biomimetic models of stratum corneum (SC), lipid monolayers and liposomes. GD-PAMAM-3 and VitC@GD-PAMAM-3 (GD-PAMAM-3 with encapsulated vitamin C) can both interact with the lipid representatives of the SC lipid matrix, whichever pH is considered. However, only pH 5.0 is suggested to be favorable to release vitamin C into the SC matrix. Their binding to SC-biomimetic liposomes revealed only a slight effect on membrane permeability in accordance with the absence of cytotoxicity but an increase in membrane rigidity, suggesting a reinforcement of the SC barrier property. Globally, our results suggest that the dendrimer GD-PAMAM-3 could be an efficient carrier for cosmetic applications.

Added Value of Biophysics to Study Lipid-Driven Biological Processes: The Case of Surfactins, a Class of Natural Amphiphile Molecules

The role of membrane lipids is increasingly claimed to explain biological activities of natural amphiphile molecules. To decipher this role, biophysical studies with biomimetic membrane models are often helpful to obtain insights at the molecular and atomic levels. In this review, the added value of biophysics to study lipid-driven biological processes is illustrated using the case of surfactins, a class of natural lipopeptides produced by Bacillus sp. showing a broad range of biological activities. The mechanism of interaction of surfactins with biomimetic models showed to be dependent on the surfactins-to-lipid ratio with action as membrane disturber without membrane lysis at low and intermediate ratios and a membrane permeabilizing effect at higher ratios. These two mechanisms are relevant to explain surfactins' biological activities occurring without membrane lysis, such as their antiviral and plant immunity-eliciting activities, and the one involving cell lysis, such as their antibacterial and hemolytic activities. In both biological and biophysical studies, influence of surfactin structure and membrane lipids on the mechanisms was observed with a similar trend. Hence, biomimetic models represent interesting tools to elucidate the biological mechanisms targeting membrane lipids and can contribute to the development of new molecules for pharmaceutical or agronomic applications.

Characterizing the lipid fingerprint of the mechanosensitive channel Piezo2

Piezo2 is a mechanosensitive ion channel that plays critical roles in sensing touch and pain, proprioception, and regulation of heart rate. Global knockout of Piezo2 leads to perinatal lethality in mice, and Piezo2 gain-of-function mutations are associated with distal arthrogryposis, a disease characterized by congenital joint contractures. Emerging evidence suggests that Piezo channels (Piezo1 and Piezo2) can be regulated by their local membrane environment and particularly by cholesterol and phosphoinositides. To characterize the local Piezo2 lipid environment and investigate key lipid-protein interactions, we carried out coarse-grained molecular dynamics simulations of Piezo2 embedded in a complex mammalian membrane containing >60 distinct lipid species. We show that Piezo2 alters its local membrane composition such that it becomes enriched with specific lipids, such as phosphoinositides, and forms specific, long-term interactions with a variety of lipids at functionally relevant sites.

Infrared Spectroscopic Study of Multi-Component Lipid Systems: A Closer Approximation to Biological Membrane Fluidity

Membranes are essential to cellular organisms, and play several roles in cellular protection as well as in the control and transport of nutrients. One of the most critical membrane properties is fluidity, which has been extensively studied, using mainly single component systems. In this study, we used Fourier transform infrared spectroscopy to evaluate the thermal behavior of multi-component supported lipid bilayers that mimic the membrane composition of tumoral and non-tumoral cell membranes, as well as microorganisms such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus. The results showed that, for tumoral and non-tumoral membrane models, the presence of cholesterol induced a loss of cooperativity of the transition. However, in the absence of cholesterol, the transitions of the multi-component lipid systems had sigmoidal curves where the gel and fluid phases are evident and where main transition temperatures were possible to determine. Additionally, the possibility of designing multi-component lipid systems showed the potential to obtain several microorganism models, including changes in the cardiolipin content associated with the resistance mechanism in Staphylococcus aureus. Finally, the potential use of multi-component lipid systems in the determination of the conformational change of the antimicrobial peptide LL-37 was studied. The results showed that LL-37 underwent a conformational change when interacting with Staphylococcus aureus models, instead of with the erythrocyte membrane model. The results showed the versatile applications of multi-component lipid systems studied by Fourier transform infrared spectroscopy.

Deciphering the role of plant plasma membrane lipids in response to invasion patterns: how could biology and biophysics help?

Plants have to constantly face pathogen attacks. To cope with diseases, they have to detect the invading pathogen as early as possible via the sensing of conserved motifs called invasion patterns. The first step of perception occurs at the plasma membrane. While many invasion patterns are perceived by specific proteinaceous immune receptors, several studies have highlighted the influence of the lipid composition and dynamics of the plasma membrane in the sensing of invasion patterns. In this review, we summarize current knowledge on how some microbial invasion patterns could interact with the lipids of the plasma membrane, leading to a plant immune response. Depending on the invasion pattern, different mechanisms are involved. This review outlines the potential of combining biological with biophysical approaches to decipher how plasma membrane lipids are involved in the perception of microbial invasion patterns.

Revealing local molecular distribution, orientation, phase separation, and formation of domains in artificial lipid layers: Towards comprehensive characterization of biological membranes

Lipids, together with molecules such as DNA and proteins, are one of the most relevant systems responsible for the existence of life. Selected lipids are able to assembly into various organized structures, such as lipid membranes. The unique properties of lipid membranes determine their complex functions, not only to separate biological environments, but also to participate in regulatory functions, absorption of nutrients, cell-cell communication, endocytosis, cell signaling, and many others. Despite numerous scientific efforts, still little is known about the reason underlying the variability within lipid membranes, and its biochemical significance. In this review, we discuss the structural complexity of lipid membranes, as well as the importance to simplify studied systems in order to understand phenomena occurring in natural, complex membranes. Such systems require a model interface to be analyzed. Therefore, here we focused on analytical studies of artificial systems at various interfaces. The molecular structure of lipid membranes, specifically the nanometric thickens of molecular bilayer, limits in a major extent the choice of highly sensitive methods suitable to study such structures. Therefore, we focused on methods that combine high sensitivity, and/or chemical selectivity, and/or nanometric spatial resolution, such as atomic force microscopy, nanospectroscopy (tip-enhanced Raman spectroscopy, infrared nanospectroscopy), phase modulation infrared reflection-absorption spectroscopy, sum-frequency generation spectroscopy. We summarized experimental and theoretical approaches providing information about molecular structure and composition, lipid spatial distribution (phase separation), organization (domain shape, molecular orientation) of lipid membranes, and real-time visualization of the influence of various molecules (proteins, drugs) on their integrity. An integral part of this review discusses the latest achievements in the field of lipid layer-based biosensors.

Antibacterial Activity of Small Molecules Which Eradicate Methicillin-Resistant Staphylococcus aureus Persisters

The serious challenge posed by multidrug-resistant bacterial infections with concomitant treatment failure and high mortality rates presents an urgent threat to the global health. We herein report the discovery of a new class of potent antimicrobial compounds that are highly effective against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). The compounds were efficiently synthesized in one-pot employing a cascade of Groebke-Blackburn-Bienaymé and aza-Michael addition reactions. Phenotypic screening of the pilot library against various bacterial species including methicillin-sensitive and MRSA strains, has identified potent chemotypes with minimal inhibitory concentrations (MIC) of 3.125-6.25 μg/ml. The most potent compounds were fast-acting at eradicating exponentially growing MRSA, with killing achieved after 30 min of exposure to the compounds. They were also able to kill MRSA persister cells which are tolerant to most available medications. Microscopic analysis using fluorescence microscope and atomic force microscope indicate that these compounds lead to disruption of bacterial cell envelopes. Most notably, bacterial resistance toward these compounds was not observed after 20 serial passages in stark contrast to the significant resistance developed rapidly upon exposure to a clinically relevant antibiotic. Furthermore, the compounds did not induce significant hemolysis to human red blood cells. In vivo safety studies revealed a high safety profile of these motifs. These small molecules hold a promise for further studies and development as new antibacterial agents against MRSA infections.

Model architectures for bacterial membranes

The complex composition of bacterial membranes has a significant impact on the understanding of pathogen function and their development towards antibiotic resistance. In addition to the inherent complexity and biosafety risks of studying biological pathogen membranes, the continual rise of antibiotic resistance and its significant economical and clinical consequences has motivated the development of numerous in vitro model membrane systems with tuneable compositions, geometries, and sizes. Approaches discussed in this review include liposomes, solid-supported bilayers, and computational simulations which have been used to explore various processes including drug-membrane interactions, lipid-protein interactions, host-pathogen interactions, and structure-induced bacterial pathogenesis. The advantages, limitations, and applicable analytical tools of all architectures are summarised with a perspective for future research efforts in architectural improvement and elucidation of resistance development strategies and membrane-targeting antibiotic mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-021-00913-7.

Topographically smooth and stable supported lipid bilayer for high-resolution AFM studies

The cellular membrane has been identified to play a critical role in various biological processes including the assembly of biological systems. Membranes are complex, primarily two-dimensional assemblies with varied lipid compositions depending on the particular region of the cell. Supported lipid bilayers are considered as appropriate models for physio-chemical studies of membranes including numerous single molecule techniques. Atomic force microscopy (AFM) as a topographic technique is a fully appropriate single molecule technique capable of direct observation of molecular processes on membranes. However, reliable experimental AFM studies require the preparation of the bilayer with a sub-nanometer smooth morphology, which remains stable over long-time observation. Here we present the methodology, which allows one to prepare a smooth, stable, structurally homogeneous lipid bilayer without the presence of any trapped vesicles. We described the application of such lipid bilayers to probe time-dependent early stages of aggregation of monomeric amyloid proteins. Importantly, the proposed methodology can be extended to bilayers with various compositions, by incorporating different lipids for on-membrane aggregation study including cholesterol. Furthermore, this methodology development allowed us to monitor the aggregation of amyloid protein at its physiologically relevant low protein concentration. The flexibility of altering the membrane composition allows to identify the specific role of a particular lipid towards the aggregation kinetics, revealing the plausible mechanism of disease development.

Simulations of Kindlin-2 PIP binding domains reveal protonation-dependent membrane binding modes

Kindlin-2, a member of the Kindlin family of peripheral membrane proteins, is important for integrin activation and stabilization of epidermal growth factor receptor. It associates with the cytoplasmic face of the plasma membrane via dedicated phosphatidylinositol phosphate binding domains located in the N-terminal F0 and Pleckstrin Homology domains. These domains have binding affinity for phosphatidylinositol 4,5-bisphosphate and, to a greater degree, phosphatidylinositol 3,4,5-trisphosphate. The biological significance of the differential binding of these phosphatidylinositol phosphates to Kindlin-2 and the mechanism by which they activate Kindlin-2 are not well understood. Recently, ssNMR identified the predominant protonation states of phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate near physiological pH in the presence of anionic lipids. Here, we perform atomistic simulation of the bound state of the Pleckstrin Homology and F0 domains of Kindlin-2 at membranes containing phosphatidylinositol 4,5-bisphosphate/phosphatidylinositol 3,4,5-trisphosphate with differing protonation states. This computational approach demonstrates that these two phosphatidylinositol phosphates differently modulate Kindlin-2 subdomain binding in a protonation-state-dependent manner. We speculate these variations in binding mode provide a mechanism for intracellular pH and Ca²⁺ influx to control the membrane binding behavior and activity of Kindlin-2.

Can oxysterols work in anti-glioblastoma therapy? Model studies complemented with biological experiments

Despite the progress made in recent years in the field of oncology, the results of glioblastoma treatment remain unsatisfactory. In this paper, cholesterol derivatives - oxysterols - have been investigated in the context of their anti-cancer activity. First, the influence of three oxysterols (7-K, 7β-OH and 25-OH), differing in their chemical structure, on the properties of a model membrane imitating glioblastoma multiforme (GBM) cells was investigated. For this purpose, the Langmuir monolayer technique was applied. The obtained results clearly show that oxysterols modify the structure of the membrane by its stiffening, with the 7-K effect being the most pronounced. Next, the influence of 7-K on the nanomechanical properties of glioblastoma cells (U-251 line) was verified with AFM. It has been shown that 7-K has a dose-dependent cytotoxic effect on glioblastoma cells leading to the induction of apoptosis as confirmed by viability tests. Interestingly, significant changes in membrane structure, characteristic for phospholipidosis, has also been observed. Based on our results we believe that oxysterol-induced apoptosis and phospholipidosis are related and may share common signaling pathways. Dysregulation of lipids in phospholipidosis inhibit cell proliferation and may play key roles in the induction of apoptosis by oxysterols. Moreover, anticancer activity of these compounds may be related to the immobilization of cancer cells as a result of stiffening effect caused by oxysterols. Therefore, we believe that oxysterols are good candidates as new therapeutic molecules as an alternative to the aggressive treatment of GBM currently in use.

Sitosterol and glucosylceramide cooperative transversal and lateral uneven distribution in plant membranes

The properties of biomembranes depend on the presence, local structure and relative distribution assumed by the thousands of components it is made of. As for animal cells, plant membranes have been demonstrated to be organized in subdomains with different persistence lengths and times. In plant cells, sitosterol has been demonstrated to confer to phospholipid membranes a more ordered structure while among lipids, glycosphingolipids are claimed to form rafts where they tightly pack with sterols. Glucosylceramides are glycosphingolipids involved in plant signalling and are essential for viability of cells and whole plant. The glucosylceramide-sitosterol structural coupling within PLPC membranes is here investigated by Langmuir films, in silico simulations and neutron reflectometry, unveiling that a strong direct interaction between the two molecules exists and governs their lateral and transversal distribution within membrane leaflets. The understanding of the driving forces governing specific molecules clustering and segregation in subdomains, such as glucosylceramide and sitosterol, have an impact on the mechanical properties of biomembranes and could reflect in the other membrane molecules partitioning and activity.

Structure-Activity Relationships of Holothuroid's Triterpene Glycosides and Some In Silico Insights Obtained by Molecular Dynamics Study on the Mechanisms of Their Membranolytic Action

The article describes the structure-activity relationships (SAR) for a broad series of sea cucumber glycosides on different tumor cell lines and erythrocytes, and an in silico modulation of the interaction of selected glycosides from the sea cucumber Eupentacta fraudatrix with model erythrocyte membranes using full-atom molecular dynamics (MD) simulations. The in silico approach revealed that the glycosides bound to the membrane surface mainly through hydrophobic interactions and hydrogen bonds. The mode of such interactions depends on the aglycone structure, including the side chain structural peculiarities, and varies to a great extent. Two different mechanisms of glycoside/membrane interactions were discovered. The first one was realized through the pore formation (by cucumariosides A₁ (40) and A₈ (44)), preceded by bonding of the glycosides with membrane sphingomyelin, phospholipids, and cholesterol. Noncovalent intermolecular interactions inside multimolecular membrane complexes and their stoichiometry differed for 40 and 44. The second mechanism was realized by cucumarioside A₂ (59) through the formation of phospholipid and cholesterol clusters in the outer and inner membrane leaflets, correspondingly. Noticeably, the glycoside/phospholipid interactions were more favorable compared to the glycoside/cholesterol interactions, but the glycoside possessed an agglomerating action towards the cholesterol molecules from the inner membrane leaflet. In silicosimulations of the interactions of cucumarioside A₇ (45) with model membrane demonstrated only slight interactions with phospholipid polar heads and the absence of glycoside/cholesterol interactions. This fact correlated well with very low experimental hemolytic activity of this substance. The observed peculiarities of membranotropic action are in good agreement with the corresponding experimental data on hemolytic activity of the investigated compounds in vitro.

Fluorescent Benzothiadiazole Derivatives as Fluorescence Imaging Dyes: A Decade of New Generation Probes

The current review describes advances in the use of fluorescent 2,1,3-benzothiadiazole (BTD) derivatives after nearly one decade since the first description of bioimaging experiments using this class of fluorogenic dyes. The review describes the use of BTD-containing fluorophores applied as, inter alia, bioprobes for imaging cell nuclei, mitochondria, lipid droplets, sensors, markers for proteins and related events, biological processes and activities, lysosomes, plasma membranes, multicellular models, and animals. A number of physicochemical and photophysical properties commonly observed for BTD fluorogenic structures are also described.

Protoplast: A Valuable Toolbox to Investigate Plant Stress Perception and Response

Plants are constantly facing abiotic and biotic stresses. To continue to thrive in their environment, they have developed many sophisticated mechanisms to perceive these stresses and provide an appropriate response. There are many ways to study these stress signals in plant, and among them, protoplasts appear to provide a unique experimental system. As plant cells devoid of cell wall, protoplasts allow observations at the individual cell level. They also offer a prime access to the plasma membrane and an original view on the inside of the cell. In this regard, protoplasts are particularly useful to address essential biological questions regarding stress response, such as protein signaling, ion fluxes, ROS production, and plasma membrane dynamics. Here, the tools associated with protoplasts to comprehend plant stress signaling are overviewed and their potential to decipher plant defense mechanisms is discussed.

Toxicity and membrane perturbation properties of the ribotoxin-like protein Ageritin

Ageritin is the prototype of a new ribotoxin-like protein family, which has been recently identified also in basidiomycetes. The protein exhibits specific RNase activity through the cleavage of a single phosphodiester bond located at sarcin/ricin loop of the large rRNA, thus inhibiting protein biosynthesis at early stages. Conversely to other ribotoxins, its activity requires the presence of divalent cations. In the present study, we report the activity of Ageritin on both prokaryotic and eukaryotic cells showing that the protein has a prominent effect on cancer cells viability and no effects on eukaryotic and bacterial cells. In order to rationalize these findings, the ability of the protein to interact with various liposomes mimicking normal, cancer and bacterial cell membranes was explored. The collected results indicate that Ageritin can interact with DPPC/DPPS/Chol vesicles, used as a model of cancer cell membranes, and with DPPC/DPPG vesicles, used as a model of bacterial cell membranes, suggesting a selective interaction with anionic lipids. However, a different perturbation of the two model membranes, mediated by cholesterol redistribution, was observed and this might be at the basis of Ageritin selective toxicity towards cancer cells.

The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux

Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.

Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules

The ability to measure the passive membrane permeation of drug-like molecules is of fundamental biological and pharmaceutical importance. Of significance, passive diffusion across the cellular membranes plays an effective role in the delivery of many pharmaceutical agents to intracellular targets. Hence, approaches for quantitative measurement of membrane permeability have been the topics of research for decades, resulting in sophisticated biomimetic systems coupled with advanced techniques. In this review, recent developments in experimental approaches along with theoretical models for quantitative and real-time analysis of membrane transport of drug-like molecules through mimetic and living cell membranes are discussed. The focus is on time-resolved fluorescence-based, surface plasmon resonance, and second-harmonic light scattering approaches. The current understanding of how properties of the membrane and permeant affect the permeation process is discussed.

Attracted to membranes: lipid-binding domains in plants

Membranes are essential for cells and organelles to function. As membranes are impermeable to most polar and charged molecules, they provide electrochemical energy to transport molecules across and create compartmentalized microenvironments for specific enzymatic and cellular processes. Membranes are also responsible for guided transport of cargoes between organelles and during endo- and exocytosis. In addition, membranes play key roles in cell signaling by hosting receptors and signal transducers and as substrates and products of lipid second messengers. Anionic lipids and their specific interaction with target proteins play an essential role in these processes, which are facilitated by specific lipid-binding domains. Protein crystallography, lipid-binding studies, subcellular localization analyses, and computer modeling have greatly advanced our knowledge over the years of how these domains achieve precision binding and what their function is in signaling and membrane trafficking, as well as in plant development and stress acclimation.

Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation

The plant plasma membrane (PM) is an essential barrier between the cell and the external environment, controlling signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols, and phospholipids. The glycosyl inositol phosphoryl ceramides (GIPCs), representing up to 40% of total sphingolipids, are assumed to be almost exclusively in the outer leaflet of the PM. However, their biological role and properties are poorly defined. In this study, we investigated the role of GIPCs in membrane organization. Because GIPCs are not commercially available, we developed a protocol to extract and isolate GIPC-enriched fractions from eudicots (cauliflower and tobacco) and monocots (leek and rice). Lipidomic analysis confirmed the presence of trihydroxylated long chain bases and 2-hydroxylated very long-chain fatty acids up to 26 carbon atoms. The glycan head groups of the GIPCs from monocots and dicots were analyzed by gas chromatograph-mass spectrometry, revealing different sugar moieties. Multiple biophysics tools, namely Langmuir monolayer, ζ-Potential, light scattering, neutron reflectivity, solid state 2H-NMR, and molecular modeling, were used to investigate the physical properties of the GIPCs, as well as their interaction with free and conjugated phytosterols. We showed that GIPCs increase the thickness and electronegativity of model membranes, interact differentially with the different phytosterols species, and regulate the gel-to-fluid phase transition during temperature variations. These results unveil the multiple roles played by GIPCs in the plant PM.

Targeted liposomal drug delivery: a nanoscience and biophysical perspective

Liposomes are a unique platform for drug delivery, and a number of liposomal formulations have already been commercialized. Doxil is a representative example, which uses PEGylated liposomes to load doxorubicin for cancer therapy. Its delivery relies on the enhanced permeability and retention (EPR) effect or passive targeting. Drug loading can be achieved using both standard liposomes and also those containing a solid core such as mesoporous silica and poly(lactide-co-glycolide) (PLGA). Developments have also been made on active targeted delivery using bioaffinity ligands such as small molecules, antibodies, peptides and aptamers. Compared to other types of nanoparticles, the surface of liposomes is fluid, allowing dynamic organization of targeting ligands to achieve optimal binding to cell surface receptors. This review article summarizes development of liposomal targeted drug delivery systems, with an emphasis on the biophysical properties of lipids. In both passive and active targeting, the effects of liposome size, charge, fluidity, rigidity, head-group chemistry and PEGylation are discussed along with recent examples. Most of the examples are focused on targeting tumors or cancer cells. Finally, a few examples of commercialized formulations are described, and some future research opportunities are discussed.

Effects of lipid heterogeneity on model human brain lipid membranes

Cell membranes naturally contain a heterogeneous lipid distribution. However, homogeneous bilayers are commonly preferred and utilised in computer simulations due to their relative simplicity, and the availability of lipid force field parameters. Recently, experimental lipidomics data for the human brain cell membranes under healthy and Alzheimer's disease (AD) conditions were investigated, since disruption to the lipid composition has been implicated in neurodegenerative disorders, including AD [R. B. Chan et al., J. Biol. Chem., 2012, 287, 2678-2688]. In order to observe the effects of lipid complexity on the various bilayer properties, molecular dynamics simulations were used to study four membranes with increasing heterogeneity: a pure POPC membrane, a POPC and cholesterol membrane in a 1 : 1 ratio (POPC-CHOL), and to our knowledge, the first realistic models of a healthy brain membrane and an Alzheimer's diseased brain membrane. Numerous structural, interfacial, and dynamical properties, including the area per lipid, interdigitation, dipole potential, and lateral diffusion of the two simple models, POPC and POPC-CHOL, were analysed and compared to those of the complex brain models consisting of 27 lipid components. As the membranes gain heterogeneity, a number of alterations were found in the structural and dynamical properties, and more significant differences were observed in the lateral diffusion. Additionally, we observed snorkeling behaviour of the lipid tails that may play a role in the permeation of small molecules across biological membranes. In this work, atomistic description of realistic brain membrane models is provided, which can add insight towards the permeability and transport pathways of small molecules across these membrane barriers.

Interactions of Cationic Diruthenium Trithiolato Complexes with Phospholipid Membranes Studied by NMR Spectroscopy

To apprehend the possible mechanisms involved in the cellular uptake and the membrane interactions of cytotoxic dinuclear p-cymene trithiolato ruthenium(II) complexes, the interactions of the complexes [(η⁶-p-MeC₆H₄Prⁱ)₂Ru₂(R¹)₂(R²)]⁺ (R¹ = R² = SC₆H₄-m-Prⁱ:1; R¹ = SC₆H₄-p-OMe, R² = SC₆H₄-p-OH:2; R¹ = SCH₂C₆H₄-p-OMe, R² = SC₆H₄-p-OH:3) with 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) vesicles and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) micelles were studied using nuclear magnetic resonance (NMR) spectroscopy. ¹H NMR, nuclear Overhauser effect (NOE), diffusion ordered spectroscopy (DOSY), and T₁ and T₂ relaxation data provided information on interactions between the complexes and the model membranes and on the submolecular localization of the complexes at the membrane interface. The results suggest that (a) the interaction takes place without new covalent adduct formation, (b) the cationic diruthenium complexes interact with DOPC head groups most likely involving electrostatic interactions while remaining structurally unchanged, (c) the changes indicating interactions are more pronounced for the most lipophilic complex 1, and (d) the diruthenium complexes remain at the exterior vesicle surface and are unlikely inserted between the phospholipid chains. The complexes also interact with micellar/free DHPC and seem to induce micellization or aggregation in solutions below critical micelle concentration (CMC). Our study suggests high affinity of the Ru complexes for the membrane surface that likely plays a key role in cellular uptake and possibly also in redistribution in mitochondria.

Lipid Membranes as Key Targets for the Pharmacological Actions of Ginsenosides

In this review, we will focus on the activity of ginsenosides on membranes and their related effects, from physicochemical, biophysical, and pharmacological viewpoints. Ginsenosides are a class of saponins with a large structural diversity and a wide range of pharmacological effects. These effects can at least partly be related to their activity on membranes which results from their amphiphilic character. Some ginsenosides are able to interact with membrane lipids and associate into nanostructures, making them possible adjuvants for vaccines. They are able to modulate membrane biophysical properties such as membrane fluidity, permeability or the formation of lateral domains with some degree of specificity towards certain cell types such as bacteria, fungi, or cancer cells. In addition, they have shown antioxidant properties which protect membranes from lipid oxidation. They further displayed some activity on membrane proteins either through direct or indirect interaction. We investigate the structure activity relationship of ginsenosides on membranes and discuss the implications and potential use as anticancer, antibacterial, and antifungal agents.

How unsaturated fatty acids and plant stanols affect sterols plasma level and cellular membranes? Review on model studies involving the Langmuir monolayer technique

The Langmuir monolayer technique has long been known for its usefulness to study the interaction between molecules and mimic cellular membranes to understand the mechanism of action of biologically relevant molecules. In this review we summarize the results that provided insight into the potential mechanism for lowering the plasma level of cholesterol by hypocholesterolemic substances (unsaturated fatty acids (UFAs) and phytocompounds) - in the aspect of prevention of atherosclerosis - and their effects on model biomembranes. The results on UFAs/cholesterol (oxysterols) interactions indicate that these systems are miscible and strongly interacting, contrary to immiscible systems containing saturated fatty acids. Lowering of cholesterol plasma level by UFAs was attributed to the strong affinity between UFAs and sterols, resulting in the formation of high stability complexes, in which sterols were bound and eliminated from the body. Studies on the effect of UFAs and plant sterols/stanols on simplified biomembranes (modeled as cholesterol/DPPC system) indicated that the studied hypocholesterolemic substances modify the biophysical properties of model membrane, affecting its fluidity and interactions between membrane components. Both UFAs and plant sterols/stanols were found to loosen interactions between DPPC and cholesterol and decrease membrane rigidity caused by the excess cholesterol in biomembrane, thus compensating strong condensing effect of cholesterol and restoring proper membrane fluidity, which is of utmost importance for normal cells functioning. The agreement between model - in vitro - studies and biological results prove the usefulness of the Langmuir monolayer technique, which helps in understanding the mode of action of biologically relevant substances.

EML webinar overview: Simulation-assisted discovery of membrane targeting nanomedicine

The COVID-19 pandemic has brought infectious diseases again to the forefront of global public health concerns. In this EML webinar (Gao, 2020), we discuss some recent work on simulation-assisted discovery of membrane targeting nanomedicine to counter increasing antimicrobial resistance and potential application of similar ideas to the current pandemic. A recent report led by the world health organization (WHO) warned that 10 million people worldwide could die of bacterial infections each year by 2050. To avert the crisis, membrane targeting antibiotics are drawing increasing attention due to their intrinsic advantage of low resistance development. In collaboration with a number of experimental groups, we show examples of simulation-assisted discovery of molecular agents capable of selectively penetrating and aggregating in bacterial lipid membranes, causing membrane permeability/rupture. Through systematic all-atom molecular dynamics simulations and free energy analysis, we demonstrate that the membrane activity of the molecular agents correlates with their ability to enter, perturb and permeabilize the lipid bilayers. Further study on different cell membranes demonstrates that the selectivity results from the presence of cholesterol in mammalian but not in bacterial membranes, as the cholesterol can condense the hydrophobic region of membrane, preventing the penetration of the molecular agents. Following the molecular penetration, we establish a continuum theory and derive the energetic driving force for the domain aggregation and pore growth on lipid membrane. We show that the energy barrier to membrane pore formation can be significantly lowered through molecular aggregation on a large domain with intrinsic curvature and a sharp interface. The theory is consistent with experimental observations and validated with coarse-grained molecular dynamics simulations of molecular domain aggregation leading to pore formation in a lipid membrane. The mechanistic modelling and simulation provide some fundamental principles on how molecular antimicrobials interact with bacterial membranes and damage them through domain aggregation and pore formation. For treating viral infections and cancer therapy, we discuss potential size- and lipid-type-based selectivity principles for developing membrane active nanomedicine. These studies suggest a general simulation-assisted platform to accelerate discovery and innovation in nanomedicine against infectious diseases. EML Webinar speakers are updated at https://imechanica.org/node/24132.

Innovaciones en la terapia antimicrobiana

La resistencia microbiana ha llevado a la búsqueda de innovadoras alternativas para su contención y dentro de las más promisorias están el uso de péptidos sintéticos, no sólo por sus características intrínsecas antimicrobianas, sino por  las interacciones sinérgicas y antagónicas que presenta con otros mediadores inmunológicos. Estas propiedades han permitido crear péptidos sintéticos reguladores de defensa innata que representan un nuevo enfoque inmunomodulador para el tratamiento de infecciones; sin embargo, sólo los diseñados con alto score antimicrobiano, han demostrado eficacia en estudios clínicos de Fase 3. Debido a su amplio espectro de actividad, un único péptido puede actuar contra bacterias Gram negativas, Gram positivas, hongos, e incluso virus y parásitos, aumentando el interés por investigar estas dinámicas moléculas.  Por otra parte, se encuentra el sistema CRISPR, para la edición de genomas bacterianos, permitirá reducir su actividad virulenta y diseñar antimicrobianos basados en nucleasas CRISPR-Cas 9 programables contra dianas específicas, las que representan un promisorio camino en el estudio de nuevas alternativas con alto potencial para eliminar la resistencia a antibióticos de bacterias altamente patógenas. Asimismo, se aborda la terapia con fagos, referida a la accion de virus que infectan bacterias, usados solos o en cocteles para aumentar el espectro de acción de estos, aprovechando su abundacia en la naturaleza, ya que se ha considerado que cada bacteria tiene un virus específico que podría emplearse como potente agente antibacteriano. Finalmente,  mientras se usen como principal medio de contención solo tratamientos convencionales antimicrobianos, incluso de manera oportuna y acertada, la microevolución en las bacterias se asegurará de seguir su curs

The Neutrally Charged Diarylurea Compound PQ401 Kills Antibiotic-Resistant and Antibiotic-Tolerant Staphylococcus aureus

Membrane-damaging antimicrobial agents have great potential to treat multidrug-resistant or multidrug-tolerant bacteria against which conventional antibiotics are not effective. However, their therapeutic applications are often hampered due to their low selectivity to bacterial over mammalian membranes or their potential for cross-resistance to a broad spectrum of cationic membrane-active antimicrobial agents. We discovered that the diarylurea derivative compound PQ401 has antimicrobial potency against multidrug-resistant and multidrug-tolerant Staphylococcus aureus. PQ401 selectively disrupts bacterial membrane lipid bilayers in comparison to mammalian membranes. Unlike cationic membrane-active antimicrobials, the neutral form of PQ401 rather than its cationic form exhibits maximum membrane activity. Overall, our results demonstrate that PQ401 could be a promising lead compound that overcomes the current limitations of membrane selectivity and cross-resistance. Also, this work provides deeper insight into the design and development of new noncharged membrane-targeting therapeutics to combat hard-to-cure bacterial infections.

Resistance or tolerance to traditional antibiotics is a challenging issue in antimicrobial chemotherapy. Moreover, traditional bactericidal antibiotics kill only actively growing bacterial cells, whereas nongrowing metabolically inactive cells are tolerant to and therefore “persist” in the presence of legacy antibiotics. Here, we report that the diarylurea derivative PQ401, previously characterized as an inhibitor of the insulin-like growth factor I receptor, kills both antibiotic-resistant and nongrowing antibiotic-tolerant methicillin-resistant Staphylococcus aureus (MRSA) by lipid bilayer disruption. PQ401 showed several beneficial properties as an antimicrobial lead compound, including rapid killing kinetics, low probability for resistance development, high selectivity to bacterial membranes compared to mammalian membranes, and synergism with gentamicin. In contrast to well-studied membrane-disrupting cationic antimicrobial low-molecular-weight compounds and peptides, molecular dynamic simulations supported by efficacy data demonstrate that the neutral form of PQ401 penetrates and subsequently embeds into bacterial lipid bilayers more effectively than the cationic form. Lastly, PQ401 showed efficacy in both the Caenorhabditis elegans and Galleria mellonella models of MRSA infection. These data suggest that PQ401 may be a lead candidate for repurposing as a membrane-active antimicrobial and has potential for further development as a human antibacterial therapeutic for difficult-to-treat infections caused by both drug-resistant and -tolerant S. aureus.

Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane

Some amphiphilic molecules are able to interact with the lipid matrix of plant plasma membranes and trigger the immune response in plants. This original mode of perception is not yet fully understood and biophysical approaches could help to obtain molecular insights. In this review, we focus on such membrane-interacting molecules, and present biophysically grounded methods that are used and are particularly interesting in the investigation of this mode of perception. Rather than going into overly technical details, the aim of this review was to provide to readers with a plant biochemistry background a good overview of how biophysics can help to study molecular interactions between bioactive amphiphilic molecules and plant lipid membranes. In particular, we present the biomimetic membrane models typically used, solid-state nuclear magnetic resonance, molecular modeling, and fluorescence approaches, because they are especially suitable for this field of research. For each technique, we provide a brief description, a few case studies, and the inherent limitations, so non-specialists can gain a good grasp on how they could extend their toolbox and/or could apply new techniques to study amphiphilic bioactive compound and lipid interactions.

Liposomal membrane permeability assessment by fluorescence techniques: Main permeabilizing agents, applications and challenges

Liposomes are lipid vesicles made of one or multiple lipid bilayers surrounding an internal aqueous core. They are broadly employed as models to study membrane structure and properties. Among these properties, liposome membrane permeability is crucial and widely assessed by fluorescence techniques. The first part of this review is devoted to describe the various techniques used for membrane permeability assessment. Attention is paid to fluorescence techniques based on vesicle leakage of self-quenching probes, dye/quencher pair or cation/ligand pair. Secondly, the membrane-active agents inducing membrane permeabilization is presented and details on their mechanisms of action are given. Emphasis is also laid on the intrinsic and extrinsic factors that can modulate the membrane permeability. Hence, a suitable liposomal membrane should be formulated according to the aim of the study and its application.

Cynara cardunculus Crude Extract as a Powerful Natural Herbicide and Insight into the Mode of Action of Its Bioactive Molecules

The use of chemical herbicides could not only potentially induce negative impacts on the environment, animals, and human health, but also increase the weed resistance to herbicides. In this context, the use of plant extracts could be an interesting and natural alternative to chemical products. It is important to understand the mode of action of their bioactive compounds. This is why we have studied the herbicidal effect of Cynara cardunculus crude extract in terms of inhibition of weeds' seedling growth and its impact on physiological parameters of treated plantlets, like conductivity, dry weight, and fluorescence, and biochemical parameters linked to oxidative stress. We have observed that C. cardunculus crude extract induces oxidative stress in the treated plants and consequently disturbs the physiological and biochemical functions of the plant cells. We have investigated the herbicidal activity of three bioactive compounds, naringenin, myricitrin, and quercetin, from the C. cardunculus crude extract. In both pre- and post-emergence trials, naringenin and myricitrin were significantly more phytotoxic than quercetin. We suggest that their differential initial interaction with the plant's plasma membrane could be one of the main signals for electrolyte leakage and production of high levels of phenoxyl radicals.