Clofazimine (CFZ) is an optically active, red-colored chemotherapeutic agent that is FDA approved... more Clofazimine (CFZ) is an optically active, red-colored chemotherapeutic agent that is FDA approved for the treatment of leprosy and is on the World Health Organization's list of essential medications. Interestingly, CFZ massively accumulates in macrophages where it forms crystal-like drug inclusions (CLDIs) after oral administration of the drug in animals and humans. The analysis of the fluorescence spectra of CLDIs formed by resident tissue macrophages revealed that CFZ, when accumulated as CLDIs, undergoes a red shift in fluorescence excitation (from Ex: 540–570 to 560–600 nm) and emission (Em: 560–580 to 640–700 nm) signal relative to the soluble and free-base crystal forms of CFZ. Using epifluorescence microscopy, CLDI(+) cells could be identified, relative to CLDI(−) cells, based on a >3-fold increment in mean fluorescence signal at excitation 640 nm and emission at 670 nm. Similarly, CLDI(+) cells could be identified by flow cytometry, based on a >100-fold increment in mean fluorescence signal using excitation lasers at 640 nm and emission detectors >600 nm. CLDI's fluorescence excitation and emission was orthogonal to that of cell viability dyes such as propidium iodide and 4,6-diamidino-2-phenylindole dihydrochloride (DAPI), cellular staining dyes such as Hoechst 33342 (nucleus) and FM 1-43 (plasma membrane), as well as many other fluorescently tagged antibodies used for immunophenotyping analyses. In vivo, >85% of CLDI(+) cells in the peritoneal exudate were F4/80(+) macrophages and >97% of CLDI(+) cells in the alveolar exudate were CD11c(+). Most importantly, the viability of cells was minimally affected by the presence of CLDIs. Accordingly, these results establish that CFZ fluorescence in CLDIs is suitable for quantitative flow cytometric phenotyping analysis and functional studies of xenobiotic sequestering macrophages.
The NCI60 human tumor cell line screen is a public resource for studying selective and non-select... more The NCI60 human tumor cell line screen is a public resource for studying selective and non-selective growth inhibition of small molecules against cancer cells. By coupling growth inhibition screening data with biological characterizations of the different cell lines, it becomes possible to infer mechanisms of action underlying some of the observable patterns of selective activity. Using these data, mechanistic relationships have been identified including specific associations between single genes and small families of closely related compounds, and less specific relationships between biological processes involving several cooperating genes and broader families of compounds. Here we aim to characterize the degree to which such specific and general relationships are present in these data. A related question is whether genes tend to act with a uniform mechanism for all associated compounds, or whether multiple mechanisms are commonly involved. We address these two issues in a statistic...
Clofazimine (CFZ) is an FDA-approved leprostatic and anti-inflammatory drug that massively accumu... more Clofazimine (CFZ) is an FDA-approved leprostatic and anti-inflammatory drug that massively accumulates in macrophages, forming insoluble, intracellular crystal-like drug inclusions (CLDIs) during long-term oral dosing. Interestingly, when added to cells in vitro, soluble CFZ is cytotoxic because it depolarizes mitochondria and induces apoptosis. Accordingly, we hypothesized that in vivo, macrophages detoxify CFZ by sequestering it in CLDIs. To test this hypothesis, CLDIs of CFZ-treated mice were biochemically isolated, and then incubated with macrophages in vitro. The cell biological effects of phagocytosed CLDIs were compared to those of soluble CFZ. Unlike soluble CFZ, phagocytosis of CLDIs did not lead to mitochondrial destabilization or apoptosis. Rather, CLDIs altered immune signaling response pathways downstream of Toll-like receptor (TLR) ligation, leading to enhanced interleukin-1 receptor antagonist (IL-1RA) production, dampened NF-κB activation and tissue necrosis factor a...
Journal of pharmaceutics & pharmacology, Jan 13, 2013
The development of computational approaches for modeling the spatiotemporal dynamics of intracell... more The development of computational approaches for modeling the spatiotemporal dynamics of intracellular, small molecule drug concentrations has become an increasingly important area of pharmaceutical research. For systems pharmacology, the system dynamics of subcellular transport can be coupled to downstream pharmacological effects on biochemical pathways that impact cell structure and function. Here, we demonstrate how a widely used systems biology modeling package - Virtual Cell - can also be used to model the intracellular, passive transport pathways of small druglike molecules. Using differential equations to represent passive drug transport across cellular membranes, spatiotemporal changes in the intracellular distribution and concentrations of exogenous chemical agents in specific subcellular organelles were simulated for weakly acidic, neutral, and basic molecules, as a function of the molecules' lipophilicity and ionization potentials. In addition, we simulated the transpo...
In pharmaceutical product development, the influence of variations in cell physiology on the tran... more In pharmaceutical product development, the influence of variations in cell physiology on the transport of drugs has important implications for strategic resource allocation and product development decisions. Here, a computational cellular pharmacokinetic model was used to explore the functional significance of intestinal cell physiology on drug absorption via passive diffusion. We simulate the effects of differences in cell physiology and
To study the chemical determinants of small molecule transport inside cells, it is crucial to vis... more To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar's distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the chemical structures of the probes and their microscopic, subcellular staining patterns. MOVID can provide a practical, graphical user interface and computer-assisted image data visualization platform to facilitate bioimage data mining and cheminformatics analysis of high content, phenotypic screening experiments.
Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging, 2007
High-throughput microscopic screening instruments can generate huge collections of images of live... more High-throughput microscopic screening instruments can generate huge collections of images of live cells incubated with combinatorial libraries of fluorescent molecules. Organizing and visualizing these images to discern biologically important patterns that link back to chemical structure is a challenge. We present an analysis and visualization methodology - Cheminformatic Assisted Image Array (CAIA) - that greatly facilitates data mining efforts. For illustration, we considered a collection of microscopic images acquired from cells incubated with each member of a combinatorial library of styryl molecules being screened for candidate bioimaging probes. By sorting CAIAs based on quantitative image features, the relative contribution of each combinatorial building block on probe intracellular distribution could be visually discerned. The results revealed trends hidden in the dataset: most interestingly, the building blocks of the styryl molecules appeared to behave as chemical address ...
The NCI60 human tumor cell line screen is a public resource for studying selective and non-select... more The NCI60 human tumor cell line screen is a public resource for studying selective and non-selective growth inhibition of small molecules against cancer cells. By coupling growth inhibition screening data with biological characterizations of the different cell lines, it becomes possible to infer mechanisms of action underlying some of the observable patterns of selective activity. Using these data, mechanistic relationships have been identified including specific associations between single genes and small families of closely related compounds, and less specific relationships between biological processes involving several cooperating genes and broader families of compounds. Here we aim to characterize the degree to which such specific and general relationships are present in these data. A related question is whether genes tend to act with a uniform mechanism for all associated compounds, or whether multiple mechanisms are commonly involved. We address these two issues in a statistical framework placing special emphasis on the effects of measurement error in the gene expression and chemical screening data. We find that as measurement accuracy increases, the pattern of apparent associations shifts from one dominated by isolated gene/compound pairs, to one in which families consisting of an average of 25 compounds are associated to the same gene. At the same time, the number of genes that appear to play a role in influencing compound activities decreases. For less than half of the genes, the presence of both positive and negative correlations indicates pleiotropic associations with molecules via different mechanisms of action.
Following extracellular drug clearance, we analyzed the rate of doxorubicin efflux from the nucle... more Following extracellular drug clearance, we analyzed the rate of doxorubicin efflux from the nucleus of three human leukemic cells (K562, Molt4 and CCRF-CEM) and related it to their differential sensitivity to this drug, after a short drug pulse. For many pulse-chase regimes, K562 cell viability was least affected by doxorubicin. In K562 cells, nuclear drug accumulation was greatest, but nuclear drug egress was also greatest. P-glycoprotein over-expression in a doxorubicin-resistant, K562/DOX sub-line did not facilitate doxorubicin efflux from the nucleus. In K562 cells, doxorubicin accumulated in multivesicular bodies (MVBs) through a pH-dependent mechanism. Inhibiting drug sequestration in MVBs did not affect nuclear efflux. The rates of doxorubicin efflux from the nuclei of live and digitonin-permeabilized K562 cells were similar. However, extracting cytoplasmic membranes with Triton X-100 significantly inhibited nuclear drug efflux following extracellular drug clearance. Our results are consistent with drug efflux from the nucleus being primarily mediated by an ATP-independent, passive diffusion mechanism. The effect of membrane extraction suggests that nonspecific drug absorption to cytoplasmic membranes plays a role in facilitating nuclear efflux in K562 cells, perhaps by lowering the concentration of free doxorubicin from a perinuclear diffusion boundary layer.
For optimizing the local, pulmonary targeting of inhaled medications, it is important to analyze ... more For optimizing the local, pulmonary targeting of inhaled medications, it is important to analyze the relationship between the physicochemical properties of small molecules and their absorption, retention and distribution in the various cell types of the airways and alveoli. A computational, multiscale, cell-based model was constructed to facilitate analysis of pulmonary drug transport and distribution. The relationship between the physicochemical properties and pharmacokinetic profile of monobasic molecules was explored. Experimental absorption data of compounds with diverse structures were used to validate this model. Simulations were performed to evaluate the effect of active transport and organelle sequestration on the absorption kinetics of compounds. Relating the physicochemical properties to the pharmacokinetic profiles of small molecules reveals how the absorption half-life and distribution of compounds are expected to vary in different cell types and anatomical regions of the lung. Based on logP, pK(a) and molecular radius, the absorption rate constants (K(a)) calculated with the model were consistent with experimental measurements of pulmonary drug absorption. The cell-based mechanistic model developed herein is an important step towards the rational design of local, lung-targeted medications, facilitating the design and interpretation of experiments aimed at optimizing drug transport properties in lung.
In the body, cell monolayers serve as permeability barriers, determining transport of molecules f... more In the body, cell monolayers serve as permeability barriers, determining transport of molecules from one organ or tissue compartment to another. After oral drug administration, for example, transport across the epithelial cell monolayer lining the lumen of the intestine determines the fraction of drug in the gut that is absorbed by the body. By modeling passive transcellular transport properties in the presence of an apical to basolateral concentration gradient, we demonstrate how a computational, cell-based molecular transport simulator can be used to define a physicochemical property space occupied by molecules with desirable permeability and intracellular retention characteristics. Considering extracellular domains of cell surface receptors located on the opposite side of a cell monolayer as a drug's desired site of action, simulation of transcellular transport can be used to define the physicochemical properties of molecules with maximal transcellular permeability but minimal intracellular retention. Arguably, these molecules would possess very desirable features: least likely to exhibit nonspecific toxicity, metabolism, and side effects associated with high (undesirable) intracellular accumulation; and most likely to exhibit favorable bioavailability and efficacy associated with maximal rates of transport across cells and minimal intracellular retention, resulting in (desirable) accumulation at the extracellular site of action. Simulated permeability values showed good correlations with PAMPA, Caco-2, and intestinal permeability measurements, without "training" the model and without resorting to statistical regression techniques to "fit" the data. Therefore, cell-based molecular transport simulators could be useful in silico screening tools for chemical genomics and drug discovery.
In pharmaceutical development, structure-activity relationship studies aim to identify characteri... more In pharmaceutical development, structure-activity relationship studies aim to identify characteristics of chemical structures associated with well-defined activity end points. While this goal-driven approach is ideally suited for lead development purposes, a more exploration-driven approach is needed to discover cell type-selective drug targeting mechanisms in complex data sets. Growth inhibition profiles across different cancer cell lines are potentially informative with respect to molecular mechanisms targeting the activity of anticancer agents to specific tumor cells, yet only a small number of mechanistic associations between chemical structure and growth inhibition profiles have been discovered to date. Here, we have applied an exhaustive statistical analysis strategy to more than 10000 compounds in the NCI's anticancer agent database to identify molecular substructures associated with specific cytotoxicity signatures against a panel of human tumor-derived cancer cell lines (the Developmental Therapeutics Program 60-cell line panel). Some of the most significant substructures conferring cell type-selective cytotoxic activity include a large family of delocalized lipophilic cations; chloropurines, chloropyrimidines, and thiazoles; organosulfur chelators and organometallic complexes; and an unexpectedly related family of alkyl-lysophospholipids and phosphate prodrugs. Information from cell-based assays and gene expression measurements have been related to substructures represented in the chemical space covered by the library, yielding several candidate targeting mechanisms.
A biophysical, computational model of cell pharmacokinetics (1CellPK) is being developed to enabl... more A biophysical, computational model of cell pharmacokinetics (1CellPK) is being developed to enable prediction of the intracellular accumulation and transcellular transport properties of small molecules using their calculated physicochemical properties as input. To test if 1CellPK can generate accurate, quantitative hypotheses and guide experimental analysis of the transcellular transport kinetics of small molecules, epithelial cells were grown on impermeable polyester membranes with cylindrical pores and chloroquine (CQ) was used as a transport probe. The effect of the number of pores and their diameter on transcellular transport of CQ was measured in apical-to-basolateral or basolateral-to-apical directions, at pH 7.4 and 6.5 in the donor compartment. Experimental and simulation results were consistent with a phospholipid bilayer-limited, passive diffusion transport mechanism. In experiments and 1CellPK simulations, intracellular CQ mass and the net rate of mass transport varied <2-fold although total pore area per cell varied >10-fold, so by normalizing the net rate of mass transport by the pore area available for transport, cell permeability on 3 mum pore diameter membranes was more than an order of magnitude less than on 0.4 mum pore diameter membranes. The results of simulations of transcellular transport were accurate for the first four hours of drug exposure, but those of CQ mass accumulation were accurate only for the first five minutes. Upon prolonged incubation, changes in cellular parameters such as lysosome pH rise, lysosome volume expansion, and nuclear shrinkage were associated with excess CQ accumulation. Based on the simulations, lysosome volume expansion alone can partly account for the measured, total intracellular CQ mass increase, while adding the intracellular binding of the protonated, ionized forms of CQ (as reflected in the measured partition coefficient of CQ in detergent-permeabilized cells at physiological pH) can further improve the intracellular CQ mass accumulation prediction.
Clofazimine (CFZ) is an optically active, red-colored chemotherapeutic agent that is FDA approved... more Clofazimine (CFZ) is an optically active, red-colored chemotherapeutic agent that is FDA approved for the treatment of leprosy and is on the World Health Organization's list of essential medications. Interestingly, CFZ massively accumulates in macrophages where it forms crystal-like drug inclusions (CLDIs) after oral administration of the drug in animals and humans. The analysis of the fluorescence spectra of CLDIs formed by resident tissue macrophages revealed that CFZ, when accumulated as CLDIs, undergoes a red shift in fluorescence excitation (from Ex: 540–570 to 560–600 nm) and emission (Em: 560–580 to 640–700 nm) signal relative to the soluble and free-base crystal forms of CFZ. Using epifluorescence microscopy, CLDI(+) cells could be identified, relative to CLDI(−) cells, based on a >3-fold increment in mean fluorescence signal at excitation 640 nm and emission at 670 nm. Similarly, CLDI(+) cells could be identified by flow cytometry, based on a >100-fold increment in mean fluorescence signal using excitation lasers at 640 nm and emission detectors >600 nm. CLDI's fluorescence excitation and emission was orthogonal to that of cell viability dyes such as propidium iodide and 4,6-diamidino-2-phenylindole dihydrochloride (DAPI), cellular staining dyes such as Hoechst 33342 (nucleus) and FM 1-43 (plasma membrane), as well as many other fluorescently tagged antibodies used for immunophenotyping analyses. In vivo, >85% of CLDI(+) cells in the peritoneal exudate were F4/80(+) macrophages and >97% of CLDI(+) cells in the alveolar exudate were CD11c(+). Most importantly, the viability of cells was minimally affected by the presence of CLDIs. Accordingly, these results establish that CFZ fluorescence in CLDIs is suitable for quantitative flow cytometric phenotyping analysis and functional studies of xenobiotic sequestering macrophages.
The NCI60 human tumor cell line screen is a public resource for studying selective and non-select... more The NCI60 human tumor cell line screen is a public resource for studying selective and non-selective growth inhibition of small molecules against cancer cells. By coupling growth inhibition screening data with biological characterizations of the different cell lines, it becomes possible to infer mechanisms of action underlying some of the observable patterns of selective activity. Using these data, mechanistic relationships have been identified including specific associations between single genes and small families of closely related compounds, and less specific relationships between biological processes involving several cooperating genes and broader families of compounds. Here we aim to characterize the degree to which such specific and general relationships are present in these data. A related question is whether genes tend to act with a uniform mechanism for all associated compounds, or whether multiple mechanisms are commonly involved. We address these two issues in a statistic...
Clofazimine (CFZ) is an FDA-approved leprostatic and anti-inflammatory drug that massively accumu... more Clofazimine (CFZ) is an FDA-approved leprostatic and anti-inflammatory drug that massively accumulates in macrophages, forming insoluble, intracellular crystal-like drug inclusions (CLDIs) during long-term oral dosing. Interestingly, when added to cells in vitro, soluble CFZ is cytotoxic because it depolarizes mitochondria and induces apoptosis. Accordingly, we hypothesized that in vivo, macrophages detoxify CFZ by sequestering it in CLDIs. To test this hypothesis, CLDIs of CFZ-treated mice were biochemically isolated, and then incubated with macrophages in vitro. The cell biological effects of phagocytosed CLDIs were compared to those of soluble CFZ. Unlike soluble CFZ, phagocytosis of CLDIs did not lead to mitochondrial destabilization or apoptosis. Rather, CLDIs altered immune signaling response pathways downstream of Toll-like receptor (TLR) ligation, leading to enhanced interleukin-1 receptor antagonist (IL-1RA) production, dampened NF-κB activation and tissue necrosis factor a...
Journal of pharmaceutics & pharmacology, Jan 13, 2013
The development of computational approaches for modeling the spatiotemporal dynamics of intracell... more The development of computational approaches for modeling the spatiotemporal dynamics of intracellular, small molecule drug concentrations has become an increasingly important area of pharmaceutical research. For systems pharmacology, the system dynamics of subcellular transport can be coupled to downstream pharmacological effects on biochemical pathways that impact cell structure and function. Here, we demonstrate how a widely used systems biology modeling package - Virtual Cell - can also be used to model the intracellular, passive transport pathways of small druglike molecules. Using differential equations to represent passive drug transport across cellular membranes, spatiotemporal changes in the intracellular distribution and concentrations of exogenous chemical agents in specific subcellular organelles were simulated for weakly acidic, neutral, and basic molecules, as a function of the molecules' lipophilicity and ionization potentials. In addition, we simulated the transpo...
In pharmaceutical product development, the influence of variations in cell physiology on the tran... more In pharmaceutical product development, the influence of variations in cell physiology on the transport of drugs has important implications for strategic resource allocation and product development decisions. Here, a computational cellular pharmacokinetic model was used to explore the functional significance of intestinal cell physiology on drug absorption via passive diffusion. We simulate the effects of differences in cell physiology and
To study the chemical determinants of small molecule transport inside cells, it is crucial to vis... more To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar's distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the chemical structures of the probes and their microscopic, subcellular staining patterns. MOVID can provide a practical, graphical user interface and computer-assisted image data visualization platform to facilitate bioimage data mining and cheminformatics analysis of high content, phenotypic screening experiments.
Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging, 2007
High-throughput microscopic screening instruments can generate huge collections of images of live... more High-throughput microscopic screening instruments can generate huge collections of images of live cells incubated with combinatorial libraries of fluorescent molecules. Organizing and visualizing these images to discern biologically important patterns that link back to chemical structure is a challenge. We present an analysis and visualization methodology - Cheminformatic Assisted Image Array (CAIA) - that greatly facilitates data mining efforts. For illustration, we considered a collection of microscopic images acquired from cells incubated with each member of a combinatorial library of styryl molecules being screened for candidate bioimaging probes. By sorting CAIAs based on quantitative image features, the relative contribution of each combinatorial building block on probe intracellular distribution could be visually discerned. The results revealed trends hidden in the dataset: most interestingly, the building blocks of the styryl molecules appeared to behave as chemical address ...
The NCI60 human tumor cell line screen is a public resource for studying selective and non-select... more The NCI60 human tumor cell line screen is a public resource for studying selective and non-selective growth inhibition of small molecules against cancer cells. By coupling growth inhibition screening data with biological characterizations of the different cell lines, it becomes possible to infer mechanisms of action underlying some of the observable patterns of selective activity. Using these data, mechanistic relationships have been identified including specific associations between single genes and small families of closely related compounds, and less specific relationships between biological processes involving several cooperating genes and broader families of compounds. Here we aim to characterize the degree to which such specific and general relationships are present in these data. A related question is whether genes tend to act with a uniform mechanism for all associated compounds, or whether multiple mechanisms are commonly involved. We address these two issues in a statistical framework placing special emphasis on the effects of measurement error in the gene expression and chemical screening data. We find that as measurement accuracy increases, the pattern of apparent associations shifts from one dominated by isolated gene/compound pairs, to one in which families consisting of an average of 25 compounds are associated to the same gene. At the same time, the number of genes that appear to play a role in influencing compound activities decreases. For less than half of the genes, the presence of both positive and negative correlations indicates pleiotropic associations with molecules via different mechanisms of action.
Following extracellular drug clearance, we analyzed the rate of doxorubicin efflux from the nucle... more Following extracellular drug clearance, we analyzed the rate of doxorubicin efflux from the nucleus of three human leukemic cells (K562, Molt4 and CCRF-CEM) and related it to their differential sensitivity to this drug, after a short drug pulse. For many pulse-chase regimes, K562 cell viability was least affected by doxorubicin. In K562 cells, nuclear drug accumulation was greatest, but nuclear drug egress was also greatest. P-glycoprotein over-expression in a doxorubicin-resistant, K562/DOX sub-line did not facilitate doxorubicin efflux from the nucleus. In K562 cells, doxorubicin accumulated in multivesicular bodies (MVBs) through a pH-dependent mechanism. Inhibiting drug sequestration in MVBs did not affect nuclear efflux. The rates of doxorubicin efflux from the nuclei of live and digitonin-permeabilized K562 cells were similar. However, extracting cytoplasmic membranes with Triton X-100 significantly inhibited nuclear drug efflux following extracellular drug clearance. Our results are consistent with drug efflux from the nucleus being primarily mediated by an ATP-independent, passive diffusion mechanism. The effect of membrane extraction suggests that nonspecific drug absorption to cytoplasmic membranes plays a role in facilitating nuclear efflux in K562 cells, perhaps by lowering the concentration of free doxorubicin from a perinuclear diffusion boundary layer.
For optimizing the local, pulmonary targeting of inhaled medications, it is important to analyze ... more For optimizing the local, pulmonary targeting of inhaled medications, it is important to analyze the relationship between the physicochemical properties of small molecules and their absorption, retention and distribution in the various cell types of the airways and alveoli. A computational, multiscale, cell-based model was constructed to facilitate analysis of pulmonary drug transport and distribution. The relationship between the physicochemical properties and pharmacokinetic profile of monobasic molecules was explored. Experimental absorption data of compounds with diverse structures were used to validate this model. Simulations were performed to evaluate the effect of active transport and organelle sequestration on the absorption kinetics of compounds. Relating the physicochemical properties to the pharmacokinetic profiles of small molecules reveals how the absorption half-life and distribution of compounds are expected to vary in different cell types and anatomical regions of the lung. Based on logP, pK(a) and molecular radius, the absorption rate constants (K(a)) calculated with the model were consistent with experimental measurements of pulmonary drug absorption. The cell-based mechanistic model developed herein is an important step towards the rational design of local, lung-targeted medications, facilitating the design and interpretation of experiments aimed at optimizing drug transport properties in lung.
In the body, cell monolayers serve as permeability barriers, determining transport of molecules f... more In the body, cell monolayers serve as permeability barriers, determining transport of molecules from one organ or tissue compartment to another. After oral drug administration, for example, transport across the epithelial cell monolayer lining the lumen of the intestine determines the fraction of drug in the gut that is absorbed by the body. By modeling passive transcellular transport properties in the presence of an apical to basolateral concentration gradient, we demonstrate how a computational, cell-based molecular transport simulator can be used to define a physicochemical property space occupied by molecules with desirable permeability and intracellular retention characteristics. Considering extracellular domains of cell surface receptors located on the opposite side of a cell monolayer as a drug's desired site of action, simulation of transcellular transport can be used to define the physicochemical properties of molecules with maximal transcellular permeability but minimal intracellular retention. Arguably, these molecules would possess very desirable features: least likely to exhibit nonspecific toxicity, metabolism, and side effects associated with high (undesirable) intracellular accumulation; and most likely to exhibit favorable bioavailability and efficacy associated with maximal rates of transport across cells and minimal intracellular retention, resulting in (desirable) accumulation at the extracellular site of action. Simulated permeability values showed good correlations with PAMPA, Caco-2, and intestinal permeability measurements, without "training" the model and without resorting to statistical regression techniques to "fit" the data. Therefore, cell-based molecular transport simulators could be useful in silico screening tools for chemical genomics and drug discovery.
In pharmaceutical development, structure-activity relationship studies aim to identify characteri... more In pharmaceutical development, structure-activity relationship studies aim to identify characteristics of chemical structures associated with well-defined activity end points. While this goal-driven approach is ideally suited for lead development purposes, a more exploration-driven approach is needed to discover cell type-selective drug targeting mechanisms in complex data sets. Growth inhibition profiles across different cancer cell lines are potentially informative with respect to molecular mechanisms targeting the activity of anticancer agents to specific tumor cells, yet only a small number of mechanistic associations between chemical structure and growth inhibition profiles have been discovered to date. Here, we have applied an exhaustive statistical analysis strategy to more than 10000 compounds in the NCI's anticancer agent database to identify molecular substructures associated with specific cytotoxicity signatures against a panel of human tumor-derived cancer cell lines (the Developmental Therapeutics Program 60-cell line panel). Some of the most significant substructures conferring cell type-selective cytotoxic activity include a large family of delocalized lipophilic cations; chloropurines, chloropyrimidines, and thiazoles; organosulfur chelators and organometallic complexes; and an unexpectedly related family of alkyl-lysophospholipids and phosphate prodrugs. Information from cell-based assays and gene expression measurements have been related to substructures represented in the chemical space covered by the library, yielding several candidate targeting mechanisms.
A biophysical, computational model of cell pharmacokinetics (1CellPK) is being developed to enabl... more A biophysical, computational model of cell pharmacokinetics (1CellPK) is being developed to enable prediction of the intracellular accumulation and transcellular transport properties of small molecules using their calculated physicochemical properties as input. To test if 1CellPK can generate accurate, quantitative hypotheses and guide experimental analysis of the transcellular transport kinetics of small molecules, epithelial cells were grown on impermeable polyester membranes with cylindrical pores and chloroquine (CQ) was used as a transport probe. The effect of the number of pores and their diameter on transcellular transport of CQ was measured in apical-to-basolateral or basolateral-to-apical directions, at pH 7.4 and 6.5 in the donor compartment. Experimental and simulation results were consistent with a phospholipid bilayer-limited, passive diffusion transport mechanism. In experiments and 1CellPK simulations, intracellular CQ mass and the net rate of mass transport varied <2-fold although total pore area per cell varied >10-fold, so by normalizing the net rate of mass transport by the pore area available for transport, cell permeability on 3 mum pore diameter membranes was more than an order of magnitude less than on 0.4 mum pore diameter membranes. The results of simulations of transcellular transport were accurate for the first four hours of drug exposure, but those of CQ mass accumulation were accurate only for the first five minutes. Upon prolonged incubation, changes in cellular parameters such as lysosome pH rise, lysosome volume expansion, and nuclear shrinkage were associated with excess CQ accumulation. Based on the simulations, lysosome volume expansion alone can partly account for the measured, total intracellular CQ mass increase, while adding the intracellular binding of the protonated, ionized forms of CQ (as reflected in the measured partition coefficient of CQ in detergent-permeabilized cells at physiological pH) can further improve the intracellular CQ mass accumulation prediction.
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Papers by Gus Rosania