Permeation of aromatic carboxylic acids across lipid bilayers: the pH-partition hypothesis revisited

Elucidating Antibiotic Permeation through the Escherichia coli Outer Membrane: Insights from Molecular Dynamics

Antibiotic resistance represents a critical public health threat, with an increasing number of Gram-negative pathogens demonstrating resistance to a broad range of clinical drugs. A primary challenge in enhancing antibiotic efficacy is overcoming the robust barrier presented by the bacterial outer membrane. Our research addresses a longstanding question: What is the rate of antibiotic permeation across the outer membrane (OM) of Gram-negative bacteria? Utilizing molecular dynamics (MD) simulations, we assess the passive permeability profiles of four commercially available antibiotics─gentamicin, novobiocin, rifampicin, and tetracycline across an asymmetric atomistic model of the Escherichia coli (E. coli) OM, employing the inhomogeneous solubility-diffusion model. Our examination of the interactions between these drugs and their environmental context during OM permeation reveals that extended hydrogen bond formation and drug-cation interactions significantly hinder the energetics of passive permeation, notably affecting novobiocin. Our MD simulations corroborate well with experimental data and reveal new implications of solvation on drug permeability, overall advancing the possible use of computational prediction of membrane permeability in future antibiotic discovery.

Improving the Accuracy of Permeability Data to Gain Predictive Power: Assessing Sources of Variability in Assays Using Cell Monolayers

The ability to predict the rate of permeation of new compounds across biological membranes is of high importance for their success as drugs, as it determines their efficacy, pharmacokinetics, and safety profile. In vitro permeability assays using Caco-2 monolayers are commonly employed to assess permeability across the intestinal epithelium, with an extensive number of apparent permeability coefficient (Papp) values available in the literature and a significant fraction collected in databases. The compilation of these Papp values for large datasets allows for the application of artificial intelligence tools for establishing quantitative structure-permeability relationships (QSPRs) to predict the permeability of new compounds from their structural properties. One of the main challenges that hinders the development of accurate predictions is the existence of multiple Papp values for the same compound, mostly caused by differences in the experimental protocols employed. This review addresses the magnitude of the variability within and between laboratories to interpret its impact on QSPR modelling, systematically and quantitatively assessing the most common sources of variability. This review emphasizes the importance of compiling consistent Papp data and suggests strategies that may be used to obtain such data, contributing to the establishment of robust QSPRs with enhanced predictive power.

Aminoglycoside uptake, stress, and potentiation in Gram-negative bacteria: new therapies with old molecules

SUMMARYAminoglycosides (AGs) are long-known molecules successfully used against Gram-negative pathogens. While their use declined with the discovery of new antibiotics, they are now classified as critically important molecules because of their effectiveness against multidrug-resistant bacteria. While they can efficiently cross the Gram-negative envelope, the mechanism of AG entry is still incompletely understood, although this comprehension is essential for the development of new therapies in the face of the alarming increase in antibiotic resistance. Increasing antibiotic uptake in bacteria is one strategy to enhance effective treatments. This review aims, first, to consolidate old and recent knowledge about AG uptake; second, to explore the connection between AG-dependent bacterial stress and drug uptake; and finally, to present new strategies of potentiation of AG uptake for more efficient antibiotic therapies. In particular, we emphasize on the connection between sugar transport and AG potentiation.

Interaction of Hoechst 33342 with POPC Membranes at Different pH Values

Hoechst 33342 (H33342) is a fluorescent probe that is commonly used to stain the DNA of living cells. To do so, it needs to interact with and permeate through cell membranes, despite its high overall charge at physiological pH values. In this work, we address the effect of pH in the association of H33342 with lipid bilayers using a combined experimental and computational approach. The partition of H33342 to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid membranes was experimentally quantified using fluorescence spectroscopy and isothermal titration calorimetry (ITC) measurements. Quantum chemical calculations were performed to select the most stable isomer of H33342 for the overall charges 0, +1, and +2, expected to predominate across the 5 < pH < 10 range. The interaction of these isomers with POPC bilayers was then studied by both unrestrained and umbrella sampling molecular dynamics (MD) simulations. Both experimental results and computational free energy profiles indicate that the partition coefficient of H33342 displays a small variation over a wide pH range, not exceeding one order of magnitude. The enthalpy variation upon partition to the membrane suggests efficient hydrogen bonding between the probe and the lipid, namely, for the protonated +2 form, which was confirmed in the MD simulation studies. The relatively high lipophilicity obtained for the charged species contrasts with the decrease in their general hydrophobicity as estimated from octanol/water partition. This highlights the distinction between lipophilicity and hydrophobicity, as well as the importance of considering the association with lipid bilayers when predicting the affinity for biomembranes.

Ligand's Partition to the Lipid Bilayer Should Be Accounted for When Estimating Their Affinity to Proteins

Ligand-protein interactions are usually studied in complex media that also contain lipids. This is particularly relevant for membrane proteins that are always associated with lipid bilayers, but also for water-soluble proteins studied in in vivo conditions. This work addresses the following two questions: (i) How does the neglect of the lipid bilayer influence the apparent ligand-protein affinity? (ii) How can the intrinsic ligand-protein affinity be obtained? Here we present a framework to quantitatively characterize ligand-protein interactions in complex media for proteins with a single binding site. The apparent affinity obtained when following some often-used approximations is also explored, to establish these approximations' validity limits and to allow the estimation of the true affinities from data reported in literature. It is found that an increase in the ligand lipophilicity or in the volume of the lipid bilayer always leads to a decrease in the apparent ligand-protein affinity, both for water-soluble and for membrane proteins. The only exceptions are very polar ligands (excluded from the lipid bilayer) and ligands whose binding affinity to the protein increases supralinearly with ligand lipophilicity. Finally, this work discusses which are the most relevant parameters to consider when exploring the specificity of membrane proteins.

Understanding Passive Membrane Permeation of Peptides: Physical Models and Sampling Methods Compared

The early characterization of drug membrane permeability is an important step in pharmaceutical developments to limit possible late failures in preclinical studies. This is particularly crucial for therapeutic peptides whose size generally prevents them from passively entering cells. However, a sequence-structure-dynamics-permeability relationship for peptides still needs further insight to help efficient therapeutic peptide design. In this perspective, we conducted here a computational study for estimating the permeability coefficient of a benchmark peptide by considering and comparing two different physical models: on the one hand, the inhomogeneous solubility-diffusion model, which requires umbrella-sampling simulations, and on the other hand, a chemical kinetics model which necessitates multiple unconstrained simulations. Notably, we assessed the accuracy of the two approaches in relation to their computational cost.

MemCross: Accelerated Weight Histogram method to assess membrane permeability

Passive permeation events across biological membranes are determining steps in the pharmacokinetics of xenobiotics. To reach an accurate and rapid prediction of membrane permeation coefficients of drugs is a complex challenge, which can efficiently support drug discovery. Such predictions are indeed highly valuable as they may guide the selection of potential leads with optimum bioavailabilities prior to synthesis. Theoretical models exist to predict these coefficients. Many of them are based on molecular dynamics (MD) simulations, which allow calculation of permeation coefficients through the evaluation of both the potential of mean force (PMF) and the diffusivity profiles. However, these simulations still require intensive computational efforts, and novel methodologies should be developed and benchmarked. Free energy perturbation (FEP) method was recently shown to estimate PMF with a significantly reduced computational cost compared to the adaptive biasing force method. This benchmarking was achieved with small molecules, namely short-chain alcohols. Here, we show that to estimate the PMF of bulkier, drug-like xenobiotics, conformational sampling is a critical issue. To reach a sufficient sampling with FEP calculations requires a relatively long time-scale, which can lower the benefits related to the computational gain. In the present work, the Accelerated Weight Histogram (AWH) method was employed for the first time in all-atom membrane models. The AWH-based protocol, named MemCross, appears affordable to estimate PMF profiles of a series of drug-like xenobiotics, compared to other enhanced sampling methods. The continuous exploration of the crossing pathway by MemCross also allows modeling subdiffusion by computing fractional diffusivity profiles. The method is also versatile as its input parameters are largely insensitive to the molecule properties. It also ensures a detailed description of the molecule orientations along the permeation pathway, picturing all intermolecular interactions at an atomic resolution. Here, MemCross was applied on a series of 12 xenobiotics, including four weak acids, and a coherent structure-activity relationship was established.

Microenvironmental pH Modification in Buccal/Sublingual Dosage Forms for Systemic Drug Delivery

Many drug candidates are poorly water-soluble. Microenvironmental pH (pH_M) modification in buccal/sublingual dosage forms has attracted increasing interest as a promising pharmaceutical strategy to enhance the oral mucosal absorption of drugs with pH-dependent solubility. Optimizing drug absorption at the oral mucosa using pH_M modification is considered to be a compromise between drug solubility and drug lipophilicity (Log D)/permeation. To create a desired pH_M around formulations during the dissolution process, a suitable amount of pH modifiers should be added in the formulations, and the appropriate methods of pH_M measurement are required. Despite pH_M modification having been demonstrated to be effective in enhancing the oral mucosal absorption of drugs, some potential risks, such as oral mucosal irritation and teeth erosion caused by the pH modifiers, should not been neglected during the formulation design process. This review aims to provide a short introduction to the pH_M modification concept in buccal/sublingual dosage forms, the properties of saliva related to pH_M modification, as well as suitable drug candidates and pH modifiers for pH_M modifying buccal/sublingual formulations. Additionally, the methods of pH_M measurement, pH_M modification methods and the corresponding challenges are summarized in the present review.

A study on attempt for determination of permeation kinetics of coumarin at lipid bilayer of liposomes by using capillary electrophoresis with moment analysis theory

It was tried to develop a moment analysis method for the determination of lipid membrane permeability. The first absolute and second central moments of elution peaks measured by liposome electrokinetic chromatography (LEKC) are analyzed by using moment equations. As a concrete example, elution peak profiles of coumarin in a LEKC system, in which liposomes consisting of 1-palmitoyl-2-oleoyl-sn‑glycero-3-phosphocholine (POPC) and phosphatidylserine (PS) are used as a pseudo-stationary phase, were analyzed. It seems that lipid membrane permeability of coumarin across the lipid bilayer of POPC/PS liposomes was measured by the moment analysis method because previous permeability measurements using parallel artificial membrane permeability assay (PAMPA) and Caco-2 cells indicated that coumarin is permeable across lipid bilayer. However, it was also pointed out that the moment analysis method with LEKC is not effective for the determination of lipid membrane permeability and that it provides information about adsorption/desorption kinetics at lipid bilayer of liposomes. Therefore, different moment equations were also developed for the determination of adsorption/desorption rate constants of coumarin from the LEKC data. It was demonstrated that permeation rate constants at lipid bilayer or adsorption/desorption rate constants can be determined from the LEKC data on the basis of moment analysis theory for the mass transfer phenomena of coumarin at the lipid bilayer of POPC/PS liposomes. Mass transfer kinetics of solutes at lipid bilayer should be determined under the conditions that liposomes originally be because they are self-assembling and dynamic systems formed through weak interactions between phospholipid monomers. The moment analysis method using LEKC is effective for the experimental determination of the mass transfer rate constants at the lipid bilayer of liposomes because neither immobilization nor chemical modification of liposomes is necessary when LEKC data are measured. It is expected that the results of this study contribute to the dissemination of an opportunity for the determination of permeation rate constants or adsorption/desorption rate constants at the lipid bilayer of liposomes to many researchers because capillary electrophoresis is widespread.

Uphill Accumulation of Ionic Species into a Lipid Vesicle by the Concentration Gradient of Counter Ions

The "uphill (against the concentration gradient)" accumulation of a hydrophobic cation (rhodamine 6G, R6G⁺) into the inner phase of a giant unilamellar vesicle (GUV) was realized with the concentration gradient of the counter anion (X^- = ClO₄^-, BF₄^-, or Br^-) in the presence of phosphate buffer (P^-, pH = 7) in the inner and outer phase of the GUV and detected as the increase of the R6G⁺ fluorescence intensity in the inner phase using a confocal laser scanning fluorescence microscope. The addition of X^- in the outer phase of the GUV caused the accumulation of R6G⁺ in the inner phase. The degree and kinetics of the accumulation were dependent on the concentration and type of X^-; e.g., the inner concentration of R6G⁺ reached 2.5 times that in the outer phase of GUV after adding 10 mM ClO₄^-. The accumulation was theoretically simulated by assuming the distribution of ion pairs (R6G⁺ and X^-, R6G⁺, and P^-) between the aqueous phase and the lipid bilayer membrane (ion pair distribution model) and the transmembrane fluxes of R6G⁺, X^- and P^-. The theoretical simulation rationalized the accumulation degree and kinetics of the experimental results. The accumulation of the target cation by the concentration gradient of the counter anion demonstrated in this study can be an effective method for the preparation of liposomal drugs.

Analysis of the Equilibrium Distribution of Ligands in Heterogeneous Media–Approaches and Pitfalls

The equilibrium distribution of small molecules (ligands) between binding agents in heterogeneous media is an important property that determines their activity. Heterogeneous systems containing proteins and lipid membranes are particularly relevant due to their prevalence in biological systems, and their importance to ligand distribution, which, in turn, is crucial to ligand’s availability and biological activity. In this work, we review several approaches and formalisms for the analysis of the equilibrium distribution of ligands in the presence of proteins, lipid membranes, or both. Special attention is given to common pitfalls in the analysis, with the establishment of the validity limits for the distinct approaches. Due to its widespread use, special attention is given to the characterization of ligand binding through the analysis of Stern–Volmer plots of protein fluorescence quenching. Systems of increasing complexity are considered, from proteins with single to multiple binding sites, from ligands interacting with proteins only to biomembranes containing lipid bilayers and membrane proteins. A new formalism is proposed, in which ligand binding is treated as a partition process, while considering the saturation of protein binding sites. This formalism is particularly useful for the characterization of interaction with membrane proteins.

Antimicrobial activity of the membrane-active compound nTZDpa is enhanced at low pH

The opportunistic human pathogen Staphylococcus aureus can evade antibiotics by acquiring antibiotic resistance genes or by entering into a non-growing dormant state. Moreover, the particular circumstances of a specific infection site, such as acidity or anaerobicity, often weaken antibiotic potency. Decreased bacterial susceptibility combined with diminished antibiotic potency is responsible for high failure rates when treating S. aureus infections. Here, we report that the membrane-active antimicrobial agent nTZDpa does not only exhibit enhanced antibiotic activity against multidrug-resistant Gram-positive pathogens in acidic pH, but also retains antimicrobial potency under anaerobic conditions. This agent completely eradicated highly antibiotic-tolerant cells and biofilms formed by methicillin-resistant S. aureus at pH 5.5 at concentrations at which it was not potent at pH 7.4. Furthermore, nTZDpa was more potent at synergistically potentiating gentamicin killing against antibiotic-tolerant MRSA cells at low pH than at high pH. All-atom molecular dynamics simulations combined with membrane-permeabilization assays revealed that the neutral form of nTZDpa, which contains carboxylic acid, is more effective than the deprotonated form at penetrating the bacterial membrane and plays an essential role in membrane activity. An acidic pH increases the proportion of the neutrally charged nTZDpa, which results in antimicrobial enhancement. Our results provide key insights into rational design of pH-sensitive membrane-active antimicrobials and antibiotic adjuvants that are effective in an infection environment. These findings demonstrate that nTZDpa is a promising lead compound for developing new therapeutics against hard-to-cure infections caused by drug-resistant and -tolerant S. aureus.

Calculation of Permeability Coefficients from Solute Equilibration Dynamics: An Assessment of Various Methods

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= β × 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.

β-cyclodextrin dendritic derivatives as permeation mediators to enhance the in vitro albendazole cysticidal activity by the improvement of the diffusion component

βCD dendritic derivatives are stable and suitable nanocarriers to enhance ABZ potency by improving solubility and permeation.

Distribution of ion pairs into a bilayer lipid membrane and its effect on the ionic permeability

This work reports the distribution constant of a target ion and a counter-ion between an aqueous phase and an artificial bilayer lipid membrane (BLM) and its influence to the ionic permeability through a BLM. A theoretical formula for ionic permeability through a BLM based on the distribution of the target ion and the counter-ion is also proposed and validated by analyzing the flux of a fluorescent cation [rhodamine 6G (R6G⁺)] through the BLM in the presence of counter-ions (X^- = Br^-, BF₄^-, and ClO₄^-). The transmembrane flux was evaluated by simultaneous measurement of the transmembrane current density and the transmembrane fluorescence intensity as a function of the membrane potential. The distribution constant of R6G⁺ and X^- between the aqueous and BLM phases was determined by a liposome-extraction method. The measured ionic permeability exhibited non-linear dependent on the aqueous concentration of R6G⁺ or X^-, but proportional to the concentration of R6G⁺ and X^- inside the BLM evaluated from the distribution constant of R6G⁺ and X^-. The proportionality demonstrates that the distribution of cations and anions between the aqueous and BLM phases dominates the flux of ion transport through the BLM. The proposed formula can express the dependence of the transmembrane current on the membrane potential and the concentrations of R6G⁺ and X^- in the aqueous phase.

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.

OATP2B1 - The underrated member of the organic anion transporting polypeptide family of drug transporters?

The organic anion transporting polypeptide 2B1 (OATP2B1) was one of the first cloned members of the SLCO family. However, its physiological and pharmacological role is still poorly understood, and object of a current debate on the transporter's relevance. Within this commentary, we summarize the data currently available on the transporter's expression and its substrates and highlight the strength and difficulties of the methods that have been applied to gather these data. The conclusion drawn from these findings was that OATP2B1 due to its intestinal expression is most likely involved in oral drug absorption of its substrate and therefore prone for interactions. This has been tested in in vivo drug interaction and/or pharmacogenetic studies. While some of these support the notion of OATP2B1 being of relevance in drug absorption, the pharmacogenetic findings are rather inconclusive. We will explain our thoughts why OATP2B1 may not influence the general systemic pharmacokinetic of certain substrates, but possibly local distribution processes, like the transfer across the blood-brain-barrier. Besides the pharmacokinetic aspects, there are data on endogenous molecules like coproporphyrins and sulfated steroids. Therefore, we will also highlight possible physiological roles of OATP2B1, which are driven by its expression pattern in the tubular cells of the kidney as well as its expression in the blood brain barrier. Finally we also deal with the advantages and disadvantages in the use of animal models to decipher the role of OATP2B1 in pharmacokinetics of its substrates and beyond.

Treatment of psoriasis with NFKBIZ siRNA using topical ionic liquid formulations

Systemic antibodies targeting tumor necrosis factor-α (TNF-α) and interleukin-17A (IL-17A) are effective in plaque psoriasis. Despite their popularity, safety concerns pose a challenge for systemic biologics. While anti-TNF-α and anti-IL-17A antibodies effectively inhibit respective proteins, we hypothesize that an approach based on local silencing of an upstream target such as NFKBIZ can be advantageous for treating psoriasis. However, effective delivery of small interfering RNA (siRNA) into the skin is a substantial hurdle due to skin's barrier function and poor stability of siRNA. Using ionic liquids as an enabling technology, we report on the effective delivery of NFKBIZ siRNA into the skin and its therapeutic efficacy in a psoriasis model. Treatment with IL-siRNA suppressed aberrant gene expression and resulted in down-regulation of psoriasis-related signals including TNF-α and IL-17A. These results provide a framework for a topical delivery platform for siRNA.

Regional Intestinal Drug Permeability and Effects of Permeation Enhancers in Rat

Sufficient colonic absorption is necessary for all systemically acting drugs in dosage forms that release the drug in the large intestine. Preclinically, colonic absorption is often investigated using the rat single-pass intestinal perfusion model. This model can determine intestinal permeability based on luminal drug disappearance, as well as the effect of permeation enhancers on drug permeability. However, it is uncertain how accurate the rat single-pass intestinal perfusion model predicts regional intestinal permeability and absorption in human. There is also a shortage of systematic in vivo investigations of the direct effect of permeation enhancers in the small and large intestine. In this rat single-pass intestinal perfusion study, the jejunal and colonic permeability of two low permeability drugs (atenolol and enalaprilat) and two high-permeability ones (ketoprofen and metoprolol) was determined based on plasma appearance. These values were compared to already available corresponding human data from a study conducted in our lab. The colonic effect of four permeation enhancers—sodium dodecyl sulfate, chitosan, ethylenediaminetetraacetic acid (EDTA), and caprate—on drug permeability and transport of chromium EDTA (an established clinical marker for intestinal barrier integrity) was determined. There was no difference in jejunal and colonic permeability determined from plasma appearance data of any of the four model drugs. This questions the validity of the rat single-pass intestinal perfusion model for predicting human regional intestinal permeability. It was also shown that the effect of permeation enhancers on drug permeability in the colon was similar to previously reported data from the rat jejunum, whereas the transport of chromium EDTA was significantly higher (p < 0.05) in the colon than in jejunum. Therefore, the use of permeation enhancers for increasing colonic drug permeability has greater risks than potential medical rewards, as indicated by the higher permeation of chromium EDTA compared to the drugs.

Intestinal Permeability and Drug Absorption: Predictive Experimental, Computational and In Vivo Approaches

The main objective of this review is to discuss recent advancements in the overall investigation and in vivo prediction of drug absorption. The intestinal permeability of an orally administered drug (given the value P_eff) has been widely used to determine the rate and extent of the drug’s intestinal absorption (F_abs) in humans. Preclinical gastrointestinal (GI) absorption models are currently in demand for the pharmaceutical development of novel dosage forms and new drug products. However, there is a strong need to improve our understanding of the interplay between pharmaceutical, biopharmaceutical, biochemical, and physiological factors when predicting F_abs and bioavailability. Currently, our knowledge of GI secretion, GI motility, and regional intestinal permeability, in both healthy subjects and patients with GI diseases, is limited by the relative inaccessibility of some intestinal segments of the human GI tract. In particular, our understanding of the complex and highly dynamic physiology of the region from the mid-jejunum to the sigmoid colon could be significantly improved. One approach to the assessment of intestinal permeability is to use animal models that allow these intestinal regions to be investigated in detail and then to compare the results with those from simple human permeability models such as cell cultures. Investigation of intestinal drug permeation processes is a crucial biopharmaceutical step in the development of oral pharmaceutical products. The determination of the intestinal P_eff for a specific drug is dependent on the technique, model, and conditions applied, and is influenced by multiple interactions between the drug molecule and the biological membranes.

Hyperpolarised NMR to follow water proton transport through membrane channels via exchange with biomolecules

Water uptake in vesicles and the subsequent exchange between water protons and amide -NH protons in amino acids can be followed by a new, highly sensitive, type of magnetic resonance spectroscopy: dynamic nuclear polarisation (DNP)-enhanced NMR in the liquid state. Water hydrogen atoms are detected prior to and after their transfer to molecular sites in peptides and proteins featuring highly-accessible proton-exchangeable groups, as is the case for the -NH groups of intrinsically disordered proteins. The detected rates for amide proton-water proton exchange can be modulated by membrane-crossing rates, when a membrane channel is interposed. We hyperpolarised water proton spins via dynamic nuclear polarisation followed by sample dissolution (d-DNP) and transferred the created polarisation to -NH groups with high solvent accessibility in an intrinsically disordered protein domain. This domain is the membrane anchor of c-Src kinase, whose activity controls cell proliferation. The hindrance of effective water proton transfer rate constants observed in free solvent when a membrane-crossing step is involved is discussed. This study aims to assess the feasibility of recently-introduced hyperpolarised (DNP-enhanced) NMR to assess water membrane crossing dynamics.

pH-permeability profiles for drug substances: Experimental detection, comparison with human intestinal absorption and modelling

The influence of pH on human intestinal absorption is frequently not considered in early drug discovery studies in the modelling and subsequent prediction of intestinal absorption for drug candidates. To bridge this gap, in this study, experimental membrane permeability data were measured for current and former drug substances with a parallel artificial membrane permeability assay (PAMPA) at different pH values (3, 5, 7.4 and 9). The presented data are in good agreement with human intestinal absorption, showing a clear influence of pH on the efficiency of intestinal absorption. For the measured data, simple and general quantitative structure-activity relationships (QSARs) were developed for each pH that makes it possible to predict the pH profiles for passive membrane permeability (i.e., a pH-permeability profile), and these predictions coincide well with the experimental data. QSARs are also proposed for the data series of highest and intrinsic membrane permeability. The molecular descriptors in the models were analysed and mechanistically related to the interaction pattern of permeability in membranes. In addition to the regression models, classification models are also proposed. All models were successfully validated and blind tested with external data. The models are available in the QsarDB repository (http://dx.doi.org/10.15152/QDB.203).

Updating molecular properties during early drug discovery

Current multiparameter optimization (MPO) strategies make use of few experimental physicochemical descriptors (i.e., solubility at physiological pH and lipophilicity in the octanol/water system). Here, we show how new trends in drug discovery (i.e., large and flexible molecules for 'difficult' targets) call for the integration of ad hoc descriptors in MPO approaches. In particular, to rank, select, and optimize drug candidates, it could be relevant to have experimental data relating to the acid-base properties and the folding of the molecule to mask polar groups (so-called 'chameleonic' properties). We propose two strategies to quantify ionization and chameleonic properties and discuss their practical integration in property criteria profiles.

Contributions of the membrane dipole potential to the function of voltage-gated cation channels and modulation by small molecule potentiators

The membrane dipole potential (Ψ_d) constitutes one of three electrical potentials generated by cell membranes. Ψ_d arises from the unfavorable parallel alignment of phospholipid and water dipoles, and varies in magnitude both longitudinally and laterally across the bilayer according to membrane composition and phospholipid packing density. In this work, we propose that dynamic counter-balancing between Ψ_d and the transmembrane potential (ΔΨ_m) governs the conformational state transitions of voltage-gated ion channels. Ψ_d consists of 1) static outer, and dynamic inner leaflet components (Ψ_d(extra) and Ψ_d(intra), respectively); and 2) a transmembrane component (ΔΨ_{d(inner-outer)}), ariing from differences in intra- and extracellular leaflet composition. Ψ_d(intra), which transitions between high and low energy states (Ψ_{d(intra, high)} and Ψ_{d(intra, low)}) as a function of channel conformation, is transduced by the pore domain. ΔΨ_{d(inner-outer)} is transduced by the voltage-sensing (VS) domain in summation with ΔΨ_m. Potentiation of voltage-gated ion channels is of interest for the treatment of cardiac, neuronal, and other disorders arising from inherited/acquired ion channel dysfunction. Potentiators are widely believed to alter the rates and voltage-dependencies of channel gating transitions by binding to pockets in the membrane-facing and other regions of ion channel targets. Here, we propose that potentiators alter Ψ_d(intra) and/or Ψ_d(extra), thereby increasing or decreasing the energy barriers governing channel gating transitions. We used quantum mechanical and molecular dynamics (MD) simulations to predict the overall Ψ_d-modulating effects of a series of published positive hERG potentiators partitioned into model DOPC bilayers. Our findings suggest a strong correlation between the magnitude of Ψ_d-lowering and positive hERG potentiation across the series.

When barriers ignore the "rule-of-five"

Why are a few drugs with properties beyond the rule of 5 (bRo5) absorbed across the intestinal mucosa while most other bRo5 compounds are not? Are such exceptional bRo5 compounds exclusively taken up by carrier-mediated transport or are they able to permeate the lipid bilayer (passive lipoidal diffusion)? Our experimental data with liposomes indicate that tetracycline, which violates one rule of the Ro5, and rifampicin, violating three of the rules, significantly permeate a phospholipid bilayer with kinetics similar to labetalol and metoprolol, respectively. Published data from experimental work and molecular dynamics simulations suggest that the formation of intramolecular H-bonds and the possibility to adopt an elongated shape besides the presence of a significant fraction of net neutral species facilitate lipid bilayer permeation. As an alternative to lipid bilayer permeation, carrier proteins can be targeted to improve absorption, with the potential drawbacks of drug-drug interactions and non-linear pharmacokinetics.

Advances in microspeciation of drugs and biomolecules: Species-specific concentrations, acid-base properties and related parameters

The pharmacokinetic and pharmacodynamic behaviour of drugs and the interacting biomolecules are highly influenced by their species-specific physico-chemical properties. The first of such bio-relevant, structure-dependent properties were the species-specific acid-base constants and the co-dependent concentrations, but the past decade brought significant advances to previously uncharted territories, including the experimental determination of species-specific partition coefficients, solubilities and redox equilibrium constants. This review gives an overview of the types and definitions of species-specific physico-chemical and analytical properties. We survey the pertinent literature, the fundamental relationships, and summarize some of our recent work that enabled the determination of species-specific partition coefficients for coexisting, inseparable protonation isomers and pH-independent, microscopic redox equilibrium constants. The thorough insight provided by these species-specific properties improves our understanding of the submolecular mechanism of pharmacokinetic processes. As a result, there are some pieces of clear-cut evidence of practical significance. A few of them are as follows: - passive diffusion into lipophilic media is not necessarily predominated by the non-charged species, contrary to the widespread misbelief. - the reactive microspecies in structure-controlled, highly specific biochemical reactions is not necessarily the major one. - a preventive defence system against oxidative stress can be based upon thiol-disulfide equilibria of custom-tailored redox potentials.

Lipid bilayer permeation of aliphatic amine and carboxylic acid drugs: rates of insertion, translocation and dissociation from MD simulations

The overabundance of drugs containing aliphatic amine and carboxylic acid groups is rationalized in terms of their membrane permeability.

Molecular simulation of nonfacilitated membrane permeation

This is a review. Non-electrolytic compounds typically cross cell membranes by passive diffusion. The rate of permeation is dependent on the chemical properties of the solute and the composition of the lipid bilayer membrane. Predicting the permeability coefficient of a solute is important in pharmaceutical chemistry and toxicology. Molecular simulation has proven to be a valuable tool for modeling permeation of solutes through a lipid bilayer. In particular, the solubility-diffusion model has allowed for the quantitative calculation of permeability coefficients. The underlying theory and computational methods used to calculate membrane permeability are reviewed. We also discuss applications of these methods to examine the permeability of solutes and the effect of membrane composition on permeability. The application of coarse grain and polarizable models is discussed. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

A liposomal fluorescence assay to study permeation kinetics of drug-like weak bases across the lipid bilayer

Lipid bilayer permeation is considered the major route for in vivo barrier passage of drugs. Despite this fact, no technique is currently available to measure the kinetics of permeation across a single lipid bilayer of structurally unrelated drug-like solutes. We developed a liposomal fluorescence assay capable to determine permeation kinetics of basic drug-like solutes across lipid bilayers. The assay is based on the hypothesis that permeation of a weak base along a concentration gradient results in net proton release at the cis-side and net proton capture at the trans-side of the bilayer. The resulting pH changes were monitored with pH-sensitive fluorophores: Test compounds were incubated with liposomes containing a pH-sensitive fluorophore at the bilayer surfaces or in the aqueous lumen and fluorescence changes were monitored with a stopped-flow apparatus in solution or by total internal reflection fluorescence microscopy with surface-captured liposomes on a microfluidic platform. Incubation with lipophilic basic drugs resulted in the expected fluorescence changes while incubation with compounds without basic functionality or high polarity did not affect fluorescence. Kinetics of fluorescence changes followed bi-exponential functions. Logarithmic permeation coefficients (logPermapp) determined in solution and by microfluidics technology showed a good correlation (r(2)=0.94, n=7) and logPermapp increased with increasing lipophilicity. Neither diffusion in the aqueous phase nor partitioning into the bilayer was rate-limiting. PEGylation of 2% of the liposomal lipids reduced Permapp by a factor ~300. In conclusion, the presented liposomal fluorescence assay is capable to determine permeation kinetics of weak basic drug-like solutes across lipid bilayers. The method is adaptable to microfluidics technology for high-throughput measurements and can potentially be modified to work for weak acid solutes.

Imaging molecular transport across lipid bilayers

Low-molecular-weight carboxylic acids have many properties common to small molecule drugs. The transport of these acids across cell membranes has been widely studied, but these studies have produced wildly varying permeability values. Recent reports have even claimed that the transport behavior of these drugs is contrary to the rule of thumb called Overton's rule, which holds that more lipophilic molecules transport across lipid membranes more quickly. We used confocal microscopy to image the transport of carboxylic acids with different lipophilicities into a giant unilamellar lipid vesicle (GUV). Fluorescein-dextran, which acts as a pH-sensitive dye, was encapsulated in the GUV to trace the transport of acid. The GUV was immobilized on the surface of a microfluidic channel by biotin-avidin binding. This microchannel allows the rapid and uniform exchange of the solution surrounding the GUV. Using a spinning-disk confocal microscope, the entire concentration field is captured in a short (<100 ms) exposure. Results show that more lipophilic acids cross the bilayer more quickly. A finite difference model was developed to simulate the experimental process and derive permeabilities. The permeabilities change with the same trend as literature oil-water partition coefficients, demonstrating that Overton's rule applies to this class of molecules.

The pH-dependent toxicity of basic pharmaceuticals in the green algae Scenedesmus vacuolatus can be explained with a toxicokinetic ion-trapping model

Several previous studies revealed that pharmaceuticals with aliphatic amine function exhibit a higher toxicity toward algae than toward other aquatic organisms. Here we investigated the pH-dependent toxicity of the five basic pharmaceuticals fluoxetine, its metabolite norfluoxetine, propranolol, lidocaine, and trimipramine. For all of them, the toxicity increased with increasing pH when aqueous effect concentrations were considered. Since these pharmaceuticals contain a basic amine group that is protonated and thus positively charged at physiological pH and because algae are capable of biological homeostasis, i.e., pH inside the algal cell remains virtually independent of variable external pH, the speciation of aliphatic amines can be different inside the algal cell compared to the external medium. Therefore, we hypothesized that the high toxicity of aliphatic amines in algae is a toxicokinetic effect caused by speciation and not a toxicodynamic effect caused by a specific mode of toxic action. This hypothesis also implies that internal effect concentrations are independent on external pH. On this basis we developed a simple toxicokinetic model, which assumes that only the neutral molecule is bioavailable and can pass the plasma membrane. This assumption is likely to be valid at pH values down to two units below the acidity constant (pK(a)). For lower pH values a more complex model would have to be evoked that includes, an, albeit smaller, permeability of the charged species. For pH>pK(a)-2, we can safely assume that the outer membrane serves as insulator and that the charged species is formed inside the cell according to the pH in the cytoplasm. Thus this toxicokinetic model is an ion-trapping model. The input parameters of this model are the measured aqueous effect concentrations determined as a function of pH and the membrane-water partitioning, which was modelled by the liposome-water partition coefficients of the neutral and cationic species. They were deduced from experimentally determined liposome-water distribution ratios at various pH values measured with an equilibrium dialysis method. The modelled internal effect concentrations were independent of the external pH and effective membrane burdens were in the same range as for other baseline toxicants found in the literature for algae, daphnids and fish. These results confirm that the higher algal toxicity of pharmaceuticals with an aliphatic amine group can be explained by a toxicokinetic effect and that these pharmaceuticals do not exhibit a specific mode of action in algae but act as baseline toxicants.

Confocal imaging to quantify passive transport across biomimetic lipid membranes

The ability of a molecule to pass through the plasma membrane without the aid of any active cellular mechanisms is central to that molecule's pharmaceutical characteristics. Passive transport has been understood in the context of Overton's rule, which states that more lipophilic molecules cross membrane lipid bilayers more readily. Existing techniques for measuring passive transport lack reproducibility and are hampered by the presence of an unstirred layer (USL) that dominates transport across the bilayer. This report describes assays based on spinning-disk confocal microscopy (SDCM) of giant unilamellar vesicles (GUVs) that allow for the detailed investigation of passive transport processes and mechanisms. This approach allows the concentration field to be directly observed, allowing membrane permeability to be determined easily from the transient concentration profile data. A series of molecules of increasing hydrophilicity was constructed, and the transport of these molecules into GUVs was observed. The observed permeability trend is consistent with Overton's rule. However, the values measured depart from the simple partition-diffusion proportionality model of passive transport. This technique is easy to implement and has great promise as an approach to measure membrane transport. It is optimally suited to precise quantitative measurements of the dependence of passive transport on membrane properties.

Real-time detection of viable microorganisms by intracellular phototautomerism

Background

To date, the detection of live microorganisms present in the environment or involved in infections is carried out by enumeration of colony forming units on agar plates, which is time consuming, laborious and limited to readily cultivable microorganisms. Although cultivation-independent methods are available, they involve multiple incubation steps and do mostly not discriminate between dead or live microorganisms. We present a novel generic method that is able to specifically monitor living microorganisms in a real-time manner.

Results

The developed method includes exposure of cells to a weak acid probe at low pH. The neutral probe rapidly permeates the membrane and enters the cytosol. In dead cells no signal is obtained, as the cytosolic pH reflects that of the acidic extracellular environment. In live cells with a neutral internal pH, the probe dissociates into a fluorescent phototautomeric anion. After reaching peak fluorescence, the population of live cells decays. This decay can be followed real-time as cell death coincides with intracellular acidification and return of the probe to its uncharged non-fluorescent state. The rise and decay of the fluorescence signal depends on the probe structure and appears discriminative for bacteria, fungi, and spores. We identified 13 unique probes, which can be applied in the real-time viability method described here. Under the experimental conditions used in a microplate reader, the reported method shows a detection limit of 10⁶ bacteria ml^-1, while the frequently used LIVE/DEAD BacLight™ Syto9 and propidium iodide stains show detection down to 10⁶ and 10⁷ bacteria ml^-1, respectively.

Conclusions

We present a novel fluorescence-based method for viability assessment, which is applicable to all bacteria and eukaryotic cell types tested so far. The RTV method will have a significant impact in many areas of applied microbiology including research on biocidal activity, improvement of preservation strategies and membrane permeation and stability. The assay allows for high-throughput applications and has great potential for rapid monitoring of microbial content in air, liquids or on surfaces.

Penetration of negatively charged lipid interfaces by the doubly deprotonated dipicolinate

The possibility that a negatively charged organic molecule penetrates the lipid interface in a reverse micellar system is examined using UV-vis absorption and NMR spectroscopy. The hypothesis that deprotonated forms of dipicolinic acid, H(2)dipic, such as Hdipic(-) and dipic(2-), can penetrate the lipid interface in a microemulsion is based on our previous finding that the insulin-enhancing anionic [VO(2)dipic](-) complex was found to reside in the hydrophobic layer of the reverse micelle (Crans et al. J. Am. Chem. Soc. 2006, 128, 4437-4445). Penetration of a polar and charged compound, namely Hdipic(-) or dipic(2-), into a hydrophobic environment is perhaps unexpected given the established rules regarding the fundamental properties of compound solubility. As such, this work has broad implications in organic chemistry and other disciplines of science. These studies required a comprehensive investigation of the different dipic species and their association in aqueous solutions at varying pH values. Combining the aqueous studies using absorption and NMR spectroscopy with those in microemulsions defines the differences observed in the heterogeneous environment. Despite the expected repulsion between the surfactant head groups and the dianionic probe molecule, these studies demonstrate that dipic resides deep in the hydrophobic portion of the reverse micellar interface. In summary, these results provide evidence that ionic molecules can reside in nonpolar locations in microheterogeneous environments. This suggests that additional factors such as solvation are important to molecule location. Documented ability to penetrate lipid surfaces of similar charge provides a rationale for why specific drugs with less than optimal hydrophobicity are successful even though they violate Lipinski's rules.

Solid-state NMR spectroscopic studies on the interaction of sorbic acid with phospholipid membranes at different pH levels

2H, 31P, and 1H-magic-angle-spinning (MAS) solid-state NMR spectroscopic methods were used to elucidate the interaction between sorbic acid, a widely used weak acid food preservative, and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayers under both acidic and neutral pH conditions. The linewidth broadening observed in the 31P NMR powder pattern spectra and the changes in the 31P longitudinal relaxation time (T1) indicate interaction with the phospholipid headgroup upon titration of sorbic acid or decanoic acid into DMPC bilayers over the pH range from 3.0 to 7.4. The peak intensities of sorbic acid decrease upon addition of paramagnetic Mn2+ ions in DMPC bilayers as recorded in the 1H MAS NMR spectra, suggesting that sorbic acid molecules are in close proximity with the membrane/aqueous surface. No significant 2H quadrupolar splitting (DeltanuQ) changes are observed in the 2H NMR spectra of DMPC-d54 upon titration of sorbic acid, and the change of pH has a slight effect on DeltanuQ, indicating that sorbic acid has weak influence on the orientation order of the DMPC acyl chains in the fluid phase over the pH range from 3.0 to 7.4. This finding is in contrast to the results of the decanoic acid/DMPC-d54 systems, where DeltanuQ increases as the concentration of decanoic acid increases. Thus, in the membrane association process, sorbic acids are most likely interacting with the headgroups and shallowly embedded near the top of the phospholipid headgroups, rather than inserting deep into the acyl chains. Thus, antimicrobial mode of action for sorbic acid may be different from that of long-chain fatty acids.

110 years of the Meyer-Overton rule: predicting membrane permeability of gases and other small compounds

The transport of gaseous compounds across biological membranes is essential in all forms of life. Although it was generally accepted that gases freely penetrate the lipid matrix of biological membranes, a number of studies challenged this doctrine as they found biological membranes to have extremely low gas-permeability values. These observations led to the identification of several membrane-embedded "gas" channels, which facilitate the transport of biological active gases, such as carbon dioxide, nitric oxide, and ammonia. However, some of these findings are in contrast to the well-established solubility-diffusion model (also known as the Meyer-Overton rule), which predicts membrane permeabilities from the molecule's oil-water partition coefficient. Herein, we discuss recently reported violations of the Meyer-Overton rule for small molecules, including carboxylic acids and gases, and show that Meyer and Overton continue to rule.

Cholesterol's decoupling effect on membrane partitioning and permeability revisited: is there anything beyond Fick's law of diffusion?

In general, Fick's law of diffusion describes membrane permeation of hydrophobic or amphiphilic molecules. In contrast to this, Thomae et al. recently identified the volume ratio between barrier and aqueous compartments as important additional determinants of membrane permeability (Pm) [A.V. Thomae, T. Koch, C. Panse, H. Wunderli-Allenspach, and S.D. Kramer, Comparing the lipid membrane affinity and permeation of drug-like acids: the intriguing effects of cholesterol and charged lipids, Pharm. Res. 24 (2007) 1457-1472.]. This new theory was supported by the striking observation that low concentrations of cholesterol increased Pm of salicylic acid. As Fick's law is of fundamental importance to all membrane transport processes, we reinvestigated this phenomenon. We measured the electrophoretic mobility of vesicles and used electrochemical scanning microscopy to study the adsorption of the SA anion to lipid vesicular bilayers and SA transport through planar lipid bilayers, respectively. As predicted by Fick's law, Pm of SA decreased continuously with increasing cholesterol content. Thomae et al. made the contrasting artifactual observation because their kinetic approach lacked the required time resolution and led to an underestimation of Pm by five orders of magnitude. We conclude that there is nothing beyond Fick's law of diffusion. It is still valid.