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Feline calicivirus (FCV), an important model for studying the biology of the Caliciviridae family, encodes the leader of the capsid (LC) protein, a viral factor known to induce apoptosis when expressed in a virus-free system. Our research has shown that the FCV LC protein forms disulfide bond-dependent homo-oligomers and exhibits intrinsic toxicity; however, it lacked a polybasic region and a transmembrane domain (TMD); thus, it was initially classified as a non-classical viroporin. The unique nature of the FCV LC protein, with no similarity to other proteins beyond the Vesivirus genus, has posed challenges for bioinformatic analysis reliant on sequence similarity. In this study, we continued characterizing the LC protein using the AlphaFold 2 and the recently released AlphaFold 3 artificial intelligence tools to predict the LC protein tertiary structure. We compared it to other molecular modeling algorithms, such as I-Tasser's QUARK, offering new insights into its putative TMD. Through exogenous interaction, we found that the recombinant LC protein associates with the CrFK plasmatic membrane and can permeate cell membranes in a disulfide bond-independent manner, suggesting that this interaction might occur through a TMD. Additionally, we examined its potential to activate the intrinsic apoptosis pathway in murine and human ovarian cancer cell lines, overexpressing survivin, an anti-apoptotic protein. All these results enhance our understanding of the LC protein's mechanism of action and suggest its role as a class-I viroporin.

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Here, we discuss a new framework developed over the last 5 years in our group to probe nanoscale membrane heterogeneity. The framework is based on the idea of characterizing lateral heterogeneity through non-affine deformation (NAD) measurements, transverse heterogeneity through three dimensional (3D) lipid packing defects, and using these approaches to formalize the seemingly trivial correlation between lateral organization and lipid packing in biological membranes. We find that measurements from NAD analysis, a prescription which is borrowed from Physics of glasses and granular material, can faithfully distinguish between liquid-ordered and disordered phases in membranes at molecular length scales and, can also be used to identify phase boundaries with high precision. Concomitantly, 3D-packing defects can not only distinguish between the two co-existing fluid phases based on their molecular scale packing (or membrane free volume), but also provide a route to connect the membrane domains to their functionality, such as exploring the molecular origins of inter-leaflet domain registration and peptide partitioning. The correlation between lateral membrane order and transverse packing presents novel molecular design-level features that can explain functions such as protein/peptide partitioning and small-molecule permeation dynamics in complex and heterogeneous membranes with high-fidelity. The framework allows us to explore the nature of lateral organization and molecular packing as a manifestation of intricate molecular interactions among a chemically rich variety of lipids and other molecules in a membrane with complex membrane composition and asymmetry across leaflets.

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The lateral stress profile of a lipid bilayer constitutes a valuable link between molecular simulation and mesoscopic elastic theory. Even though it is frequently calculated in simulations, its statistical precision (or that of observables derived from it) is often left unspecified. This omission can be problematic, as uncertainties are prerequisite to assessing statistical significance. In this chapter, we provide a comprehensive yet accessible overview of the statistical error analysis for the lateral stress profile. We detail two relatively simple but powerful techniques for generating error bars: block-averaging and bootstrapping. Combining these methods allows us to reliably estimate uncertainties, even in the presence of both temporal and spatial correlations, which are ubiquitous in simulation data. We illustrate these techniques with simple examples like stress moments, but also more complex observables such as the location of stress profile extrema and the monolayer neutral surface.

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A widespread strategy to increase the transport of therapeutic peptides across cellular membranes has been to attach lipid moieties to the peptide backbone (lipidation) to enhance their intrinsic membrane interaction. Efforts in vitro and in vivo investigating the correlation between lipidation characteristics and peptide membrane translocation efficiency have traditionally relied on end-point read-out assays and trial-and-error-based optimization strategies. Consequently, the molecular details of how therapeutic peptide lipidation affects it's membrane permeation and translocation mechanisms remain unresolved. Here we employed salmon calcitonin as a model therapeutic peptide and synthesized nine double lipidated analogs with varying lipid chain lengths. We used single giant unilamellar vesicle (GUV) calcein influx time-lapse fluorescence microscopy to determine how tuning the lipidation length can lead to an All-or-None GUV filling mechanism, indicative of a peptide mediated pore formation. Finally, we used a GUVs-containing-inner-GUVs assay to demonstrate that only peptide analogs capable of inducing pore formation show efficient membrane translocation. Our data provided the first mechanistic details on how therapeutic peptide lipidation affects their membrane perturbation mechanism and demonstrated that fine-tuning lipidation parameters could induce an intrinsic pore-forming capability. These insights and the microscopy based workflow introduced for investigating structure-function relations could be pivotal for optimizing future peptide design strategies.

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The functional analysis of protein nanopores is typically conducted in planar lipid bilayers or liposomes exploiting high-resolution but low-throughput electrical and optical read-outs. Yet, the reconstitution of protein nanopores in vitro still constitutes an empiric and low-throughput process. Addressing these limitations, nanopores can now be analyzed using the functional nanopore (FuN) screen exploiting genetically encoded fluorescent protein sensors that resolve distinct nanopore-dependent Ca2+ in- and efflux patterns across the inner membrane of Escherichia coli. With a primary proof-of-concept established for the S2168 holin, and thereof based recombinant nanopore assemblies, the question arises to what extent alternative nanopores can be analyzed with the FuN screen and to what extent alternative fluorescent protein sensors can be adapted. Focusing on self-assembling membrane peptides, three sets of 13 different nanopores are assessed for their capacity to form nanopores in the context of the FuN screen. Nanopores tested comprise both natural and computationally designed nanopores. Further, the FuN screen is extended to K+-specific fluorescent protein sensors and now provides a capacity to assess the specificity of a nanopore or ion channel. Finally, a comparison to high-resolution biophysical and electrophysiological studies in planar lipid bilayers provides an experimental benchmark for future studies.

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The global challenge of antibiotic resistance necessitates the introduction of more effective antibiotics. Here we report a potentially general design strategy, exemplified with vancomycin, that improves and expands antibiotic performance. Vancomycin is one of the most important antibiotics in use today for the treatment of Gram-positive infections. However, it fails to eradicate difficult-to-treat biofilm populations. Vancomycin is also ineffective in killing Gram-negative bacteria due to its inability to breach the outer membrane. Inspired by our seminal studies on cell penetrating guanidinium-rich transporters (e.g., octaarginine), we recently introduced vancomycin conjugates that effectively eradicate Gram-positive biofilm bacteria, persister cells and vancomycin-resistant enterococci (with V-r8, vancomycin-octaarginine), and Gram-negative pathogens (with V-R, vancomycin-arginine). Having shown previously that the spatial array (linear versus dendrimeric) of multiple guanidinium groups affects cell permeation, we report here for the first time vancomycin conjugates with dendrimerically displayed guanidinium groups that exhibit superior efficacy and breadth, presenting the best activity of V-r8 and V-R in single broad-spectrum compounds active against ESKAPE pathogens. Mode-of-action studies reveal cell-surface activity and enhanced vancomycin-like killing. The vancomycin-polyguanidino dendrimer conjugates exhibit no acute mammalian cell toxicity or hemolytic activity. Our study introduces a new class of broad-spectrum vancomycin derivatives and a general strategy to improve or expand antibiotic performance through combined mode-of-action and function-oriented design studies.

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Because of the increasing sophistication of formulation technology and the increasing polymerization of compounds directed toward undruggable drug targets, the influence of the mucus layer on gastrointestinal drug absorption has received renewed attention. Therefore, understanding the complex structure of the mucus layer containing highly glycosylated glycoprotein mucins, lipids bound to the mucins, and water held by glycans interacting with each other is critical. Recent advances in cell culture and engineering techniques have led to the development of evaluation systems that closely mimic the ecological environment and have been applied to the evaluation of gastrointestinal drug absorption while considering the mucus layer. This review provides a better understanding of the mucus layer components and the gastrointestinal tract's biological defense barrier, selects an assessment system for drug absorption in the mucus layer based on evaluation objectives, and discusses the overview and features of each assessment system.

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Background and Purpose: Physiologically-based biopharmaceutics modeling (PBBM) has been widely used to predict the oral absorption of drugs. However, the prediction of food effects on oral drug absorption is still challenging, especially for negative food effects. Marked negative food effects have been reported in most cases of quaternary ammonium compounds (QAC). However, the mechanism has remained unclear. The purpose of the present study was to investigate the bile micelle and food binding of QACs as a mechanism of the negative food effect. Experimental Approach: Trospium (TRS), propantheline (PPT), and ambenonium (AMB) were selected as model QAC drugs. The oral absorption of these QACs has been reported to be reduced by 77% (TRS), > 66% (PPT), and 79% (AMB), when taken with food. The fasted and fed state simulated intestinal fluids (FaSSIF and FeSSIF, containing 3 and 15 mM taurocholic acid, respectively) with or without FDA breakfast homogenate (BFH) were used as the simulated intestinal fluid. The unbound fraction (fu) of the QACs in these media was measured by dynamic dialysis. Key Results: The fu ratios (FeSSIF/ FaSSIF) were 0.67 (TRS), 0.47 (PPT), and 0.76 (AMB). When BFH was added to FeSSIF, it was reduced to 0.39 (TRS), 0.28 (PPT), and 0.59 (AMB). Conclusion: These results suggested that bile micelle and food binding play an important role in the negative food effect on the oral absorption of QACs.

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Silica nanoparticles (SNP) have gained tremendous attention in the recent decades. They have been used in many different biomedical fields including diagnosis, biosensing and drug delivery. Medical uses of SNP for anti-cancer, anti-microbial and theranostic applications are especially prominent due to their exceptional performance to deliver many different small molecules and recently biologics (mRNA, siRNA, antigens, antibodies, proteins, and peptides) at targeted sites. The physical and chemical properties of SNP such as large specific surface area, tuneable particle size and porosity, excellent biodegradability and biocompatibility make them an ideal drug delivery and diagnostic platform. Based on the available data and the pre-clinical performance of SNP, recent interest has driven these innovative materials towards clinical application with many of the formulations already in Phase I and Phase II trials. Herein, the progress of SNP in biomedical field is reviewed, and their safety aspects are analysed. Importantly, we critically evaluate the key structural characteristics of SNP to overcome different biological barriers including the blood-brain barrier (BBB), skin, tumour barrier and mucosal barrier. Future directions, potential pathways, and target areas towards rapid clinical translation of SNP are also recommended.

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Porphyrin, which shows selective accumulation in cancer cells, has attracted attention as a drug carrier. The influences of the functional porphyrin positions (ß- and meso-positions) on porphyrin accumulation must be understood. In this work, we focused on the investigation of the phenyl functional group whose ß-position influences cancer cell accumulation through direct membrane permeation and endocytosis. The endocytic pathway, in particular, is influenced by both clathrin-dependent and caveolae-dependent endocytosis.

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Mycolactone is an exotoxin produced by Mycobacterium ulcerans that causes the neglected tropical skin disease Buruli ulcer. This toxin inhibits the Sec61 translocon in the endoplasmic reticulum (ER), preventing the host cell from producing several secretory and transmembrane proteins, resulting in cytotoxic and immunomodulatory effects. Interestingly, only one of the two dominant isoforms of mycolactone is cytotoxic. Here, we investigate the origin of this specificity by performing extensive molecular dynamics (MD) simulations with enhanced free energy sampling to query the association trends of the two isoforms with both the Sec61 translocon, using two distinct cryo-electron microscopy (cryo-EM) models as references, and the ER membrane, which serves as a toxin reservoir prior to association. Our results suggest that mycolactone B (the cytotoxic isoform) has a stronger association with the ER membrane than mycolactone A due to more favorable interactions with membrane lipids and water molecules. This could increase the reservoir of toxin proximal to the Sec61 translocon. In one model of Sec61 inhibited by mycolactone, we find that isomer B interacts more closely with residues thought to play a key role in signal peptide recognition and, thus, are essential for subsequent protein translocation. In the other model, we find that isomer B interacts more closely with the lumenal and lateral gates of the translocon, the dynamics of which are essential for protein translocation. These interactions induce a more closed conformation, which has been suggested to block signal peptide insertion and subsequent protein translocation. Collectively, these findings suggest that isomer B's unique cytotoxicity is a consequence of both increased localization to the ER membrane and channel-locking association with the Sec61 translocon, facets that could be targeted in the development of Buruli Ulcer diagnostics and Sec61-targeted therapeutics.

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The intestinal compartment ensures nutrient absorption and barrier function against pathogens. Despite decades of research on the complexity of the gut, the adaptive potential to physical cues, such as those derived from interaction with particles of different shapes, remains less understood. Taking advantage of the technological versatility of silica nanoparticles, spherical, rod-shaped, and virus-like materials were synthesized. Morphology-dependent interactions were studied on differentiated Caco-2/HT29-MTX-E12 cells. Contributions of shape, aspect ratio, surface roughness, and size were evaluated considering the influence of the mucus layer and intracellular uptake pathways. Small particle size and surface roughness favored the highest penetration through the mucus but limited interaction with the cell monolayer and efficient internalization. Particles of a larger aspect ratio (rod-shaped) seemed to privilege paracellular permeation and increased cell-cell distances, albeit without hampering barrier integrity. Inhibition of clathrin-mediated endocytosis and chemical modulation of cell junctions effectively tuned these responses, confirming morphology-specific interactions elicited by bioinspired silica nanomaterials.

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Computer-aided drug design (CADD) approaches are playing an increasingly important role in understanding the fundamentals of ligand-receptor interactions and helping medicinal chemists design therapeutics. About 5 years ago, we presented a chapter devoted to an overview of CADD methods and covered typical CADD protocols including structure-based drug design (SBDD) and ligand-based drug design (LBDD) approaches that were frequently used in the antibiotic drug design process. Advances in computational hardware and algorithms and emerging CADD methods are enhancing the accuracy and ability of CADD in drug design and development. In this chapter, an update to our previous chapter is provided with a focus on new CADD approaches from our laboratory and other peers that can be employed to facilitate the development of antibiotic therapeutics.

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The traditional model Franz diffusion cell method has always been the “gold standard” for evaluating the permeability of transdermal drug delivery system （TDDS） drug. However， in the high throughput screening of a large number of drug molecules， it has the disadvantages of low efficiency， high cost， difficulty to obtain isolated skin，poor reliability and large workload. The emergence of parallel artificial membrane permeation assay （PAMPA） model provides reliable pre-prediction data for the evaluation of permeability of TDDS drug. PAMPA model has been widely used in the permeability screening research of TDDS drugs and their preparations such as analgesics， local anesthetics， antioxidants， antipyretics， analgesics and anti-inflammatory drugs， vitamins， cholinesterase inhibitors， active ingredients of natural products， and has the characteristics of high reliability， good selectivity， high efficiency， low cost and data stability. PAMPA model has greatly improved the high throughput screening efficiency of TDDS drug permeability. With the extensive application and gradual maturity of this model， it will become a new and effective evaluation method in addition to the traditional evaluation model.

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The development of new composite membranes is required to separate chemical species from aggressive environments without using corrective reagents. One such case is represented by the high hydrochloric acid mixture (very low pH and pCl) that contains mixed metal ions, or that of copper, cadmium, zinc and lead ions in a binary mixture (Cu-Zn and Cd-Pb) or quaternary mixture. This paper presents the obtaining of a composite membrane chitosan (Chi)-sulfonated poly (ether ether ketone) (sPEEK)-polypropylene hollow fiber (Chi/sPEEK/PPHF) and its use in the separation of binary or quaternary mixtures of copper, cadmium, zinc, and lead ions by nanofiltration and pertraction. The obtained membranes were morphologically and structurally characterized using scanning electron microscopy (SEM), high resolution SEM (HR-SEM), energy dispersive spectroscopy analysis (EDAX), Fourier Transform InfraRed (FTIR) spectroscopy, thermogravimetric analysis, and differential scanning calorimetry (TGA-DSC), but also used in preliminary separation tests. Using the ion solutions in hydrochloric acid 3 mol/L, the separation of copper and zinc or cadmium and lead ions from binary mixtures was performed. The pertraction results were superior to those obtained by nanofiltration, both in terms of extraction efficiency and because at pertraction, the separate cation was simultaneously concentrated by an order of magnitude. The mixture of the four cations was separated by nanofiltration (at 5 bars, using a membrane of a 1 m2 active area) by varying two operational parameters: pH and pCl. Cation retention could reach 95% when adequate values of operational parameters were selected. The paper makes some recommendations for the use of composite membranes, chitosan (Chi)-sulfonated poly (ether ether ketone) (sPEEK)-polypropylene hollow fiber (Chi/sPEEK/PPHF), so as to obtain the maximum possible retention of the target cation.

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Predicting the rate at which substances permeate membrane barriers in vivo is crucial for drug development. Permeability coefficients obtained from in vitro studies are valuable for this goal. These are normally determined by following the dynamics of solute equilibration between two membrane-separated compartments. However, the correct calculation of permeability coefficients from such data is not always straightforward. To address these problems, here we develop a kinetic model for solute permeation through lipid membrane barriers that includes the two membrane leaflets as compartments in a four-compartment model. Accounting for solute association with the membrane allows assessing various methods in a wide variety of conditions. The results showed that the often-used expression Papp = ß × r/3 is inapplicable to very large or very small vesicles, to moderately or highly lipophilic solutes, or when the development of a significant pH gradient opposes the solute's flux. We establish useful relationships that overcome these limitations and allow predicting permeability in compartmentalised in vitro or in vivo systems with specific properties. Finally, from the parameters for the interaction of the solute with the membrane barrier, we defined an intrinsic permeability coefficient that facilitates quantitative comparisons between solutes.

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When searching for new antibiotics against Gram-negative bacterial infections, a better understanding of the permeability across the cell envelope and tools to discriminate high from low bacterial bioavailability compounds are urgently needed. Inspired by the phospholipid vesicle-based permeation assay (PVPA), which is designed to predict non-facilitated permeation across phospholipid membranes, outer membrane vesicles (OMVs) of Escherichia coli either enriched or deficient of porins are employed to coat filter supports for predicting drug uptake across the complex cell envelope. OMVs and the obtained in vitro model are structurally and functionally characterized using cryo-TEM, SEM, CLSM, SAXS, and light scattering techniques. In vitro permeability, obtained from the membrane model for a set of nine antibiotics, correlates with reported in bacterio accumulation data and allows to discriminate high from low accumulating antibiotics. In contrast, the correlation of the same data set generated by liposome-based comparator membranes is poor. This better correlation of the OMV-derived membranes points to the importance of hydrophilic membrane components, such as lipopolysaccharides and porins, since those features are lacking in liposomal comparator membranes. This approach can offer in the future a high throughput screening tool with high predictive capacity or can help to identify compound- and bacteria-specific passive uptake pathways.

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The quantification of drug in living cells is of increasing interest in pharmaceutical research because of its importance in understanding drug efficacy and toxicity. Label-free in situ measurement methods are advantageous for their ability to obtain chemical and time profiles without the need of labelling or extraction steps. We have previously shown that Fourier transform infrared (FTIR) spectroscopy has the potential to quantify drug in situ within living cells at micromolar level when a simple solution of drug was added to the medium. The purpose of this study was to demonstrate that the approach can evaluate more complex systems such as the effect of membrane modification by a formulation on drug uptakes. The inhaled corticosteroid, beclomethasone dipropionate (BDP), in Calu-3 respiratory epithelial cells in the absence and presence of glycerol, an excipient in some inhaled medicines was used as the model system. The FTIR method was first validated for limit of detection (LOD) and quantification (LOQ) according to published guidelines and the LOQ was found to be âˆ¼ 20 µM, good enough to quantify BDP in the living cell. The uptake of BDP by living Calu-3 cells was found to be reduced in the presence of glycerol as expected due to the stiffening of the cell membrane by the presence of glycerol in the formulation. This study demonstrates the valuable analytical capability of live-cell FTIR to study the effect of formulation on drug transport in lungs and to evaluate drug availability to intracellular targets. We conclude that FTIR has potential to contribute widely at the frontier of live-cell studies.

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The study of enzyme kinetics in drug metabolism involves assessment of rates of metabolism and inhibitory potencies over a suitable concentration range. In all but the very simplest in vitro system, these drug concentrations can be influenced by a variety of nonspecific binding reservoirs that can reduce the available concentration to the enzyme system(s) under investigation. As a consequence, the apparent kinetic parameters, such as Km or Ki, that are derived can deviate from the true values. There are a number of sources of these nonspecific binding depots or barriers, including membrane permeation and partitioning, plasma or serum protein binding, and incubational binding. In the latter case, this includes binding to the assay apparatus as well as biological depots, depending on the characteristics of the in vitro matrix being used. Given the wide array of subcellular, cellular, and recombinant enzyme systems utilized in drug metabolism, each of these has different components which can influence the free drug concentration. The physicochemical properties of the test compound are also paramount in determining the influential factors in any deviation between true and apparent kinetic behavior. This chapter describes the underlying mechanisms determining the free drug concentration in vitro and how these factors can be accounted for in drug metabolism studies, illustrated with case studies from the literature.

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We developed an assay system to evaluate the cytochrome P450 (CYP) 3A4-inhibitory activity of compounds, taking account of their cellular permeability, using intestine-derived cell lines pre-treated with the CYP3A4 inducer 1α,25-dihydroxy-vitamin D3 (250 nM).Ketoconazole (KTZ), saquinavir (SQV), naringin, naringenin (NGE), bergamottin (BG), 6',7'-dihydroxybergamottin (DHBG), epigallocatechin gallate (EGCG), and resveratrol (RES) were evaluated as known CYP3A4 inhibitors. The apparent IC50 (IC50,app) values of known inhibitors were determined in Caco-2 cells with 10 µM midazolam as a CYP3A4 substrate, and compared with the IC50 values in a human liver microsome assay.SQV and BG with high lipophilicity and good membrane permeability show similar concentrations inside and outside the cells, and consequently IC50,app and IC50 are similar.KTZ, EGCG, DHBG, NGE, and RES showed a difference between IC50 and IC50,app. This is considered to result from a difference between the intracellular and extracellular concentrations of the compound, which is likely due to the involvement of efflux and/or influx transporters.This method to evaluate CYP inhibition taking account of membrane permeation should be helpful to assess the potential clinical relevance of drug-drug or drug-food interactions in the gastrointestinal tract.

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