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1.  Computational Approaches to Analyze and Predict Small Molecule Transport and Distribution at Cellular and Subcellular Levels 
Quantitative structure-activity relationship (QSAR) studies and mechanistic mathematical modeling approaches have been independently employed for analyzing and predicting the transport and distribution of small molecule chemical agents in living organisms. Both of these computational approaches have been useful to interpret experiments measuring the transport properties of small molecule chemical agents, in vitro and in vivo. Nevertheless, mechanistic cell-based pharmacokinetic models have been especially useful to guide the design of experiments probing the molecular pathways underlying small molecule transport phenomena. Unlike QSAR models, mechanistic models can be integrated from microscopic to macroscopic levels, to analyze the spatiotemporal dynamics of small molecule chemical agents from intracellular organelles to whole organs, well beyond the experiments and training data sets upon which the models are based. Based on differential equations, mechanistic models can also be integrated with other differential equations-based systems biology models of biochemical networks or signaling pathways. Although the origin and evolution of mathematical modeling approaches aimed at predicting drug transport and distribution has occurred independently from systems biology, we propose that the incorporation of mechanistic cell-based computational models of drug transport and distribution into a systems biology modeling framework is a logical next-step for the advancement of systems pharmacology research.
doi:10.1002/bdd.1879
PMCID: PMC3947293  PMID: 24218242
Cellular pharmacokinetics; Computational modeling; Drug Transport; Systems pharmacology
2.  Denoising MR Images Using Non-Local Means Filter with Combined Patch and Pixel Similarity 
PLoS ONE  2014;9(6):e100240.
Denoising is critical for improving visual quality and reliability of associative quantitative analysis when magnetic resonance (MR) images are acquired with low signal-to-noise ratios. The classical non-local means (NLM) filter, which averages pixels weighted by the similarity of their neighborhoods, is adapted and demonstrated to effectively reduce Rician noise without affecting edge details in MR magnitude images. However, the Rician NLM (RNLM) filter usually blurs small high-contrast particle details which might be clinically relevant information. In this paper, we investigated the reason of this particle blurring problem and proposed a novel particle-preserving RNLM filter with combined patch and pixel (RNLM-CPP) similarity. The results of experiments on both synthetic and real MR data demonstrate that the proposed RNLM-CPP filter can preserve small high-contrast particle details better than the original RNLM filter while denoising MR images.
doi:10.1371/journal.pone.0100240
PMCID: PMC4059740  PMID: 24933024
3.  Diabetic macular edema: new concepts in patho-physiology and treatment 
Cell & Bioscience  2014;4:27.
Diabetic macular edema (DME), a serious eye complication caused primarily by hyperglycemia, is one of the major causes of blindness. DME, which is characterized by cystic retinal thickening or lipid deposition, is prone to relapse after successful treatment. DME is a complex pathological process caused by multiple factors, including breakdown of the inner and outer blood-retinal barriers, oxidative stress, and elevated levels of vascular endothelial growth factor which have been demonstrated in both preclinical and clinical studies. Starling’s law theory explains many of the features of DME. Early detection and treatment of DME can prevent vision loss. Current effective interventions for DME include treatment of systemic risk factors, such as elevated blood glucose, blood pressure and dyslipidemia. Ophthalmic treatments include laser photocoagulation, surgery and intraocular pharmacotherapy. New drugs, which are given by intraocular injection, have emerged in recent years to become first line treatment for DME that affects the central macula with loss of vision. Laser photocoagulation is still the gold standard of treatment for DME which does not involve the central macular. This review outlines these new treatments with particular emphasis on the optimal timing of how they are given.
doi:10.1186/2045-3701-4-27
PMCID: PMC4046142  PMID: 24955234
Diabetic retinopathy; Microvasculopathy; Neuronal degenerative diseases; Therapeutic strategy; Apoptosis
4.  Expression and characterization of a soluble VEGF receptor 2 protein 
Cell & Bioscience  2014;4:14.
Objective
To clone and express a truncated, soluble vascular endothelial growth factor receptor 2 (sVEGFR2) possessing the combined-functional domains 1–3 and 5 in eukaryotic cells and to test the inhibitory effects of full length VEGFR2 in vivo.
Results
pCMV6-trunctated-rVegfr2 (6100 bp) was successfully cloned. The transfection experiments showed that either pCMV6-truncated-rat-Vegfr2 (pCMV6-truncated-rVegfr2) or pCMV6-rVegfr2 inhibited the expression of intracellular green fluorescent protein, which is usually used as an exogenous transfected reporter gene to determine the transfected efficiency. An analysis of the transfected cells revealed that the amount of full-length VEGFR2 protein in the pCMV6-truncated-rVegfr2 transfected cells was 20% lower than that in the negative control (non-transfected HEK 293 cells). The differences in test results between the transfected and negative control groups were greatest from 24–30 h after transfection; this period was therefore chosen as optimal for collecting culture supernatants. This analysis was highly sensitive for detecting the amount of sVEGFR2 protein expressed and secreted by the cells, and the sVEGFR2 protein content was found to increase by approximately 26% in the transfected cells compared to that in the negative control cells (68.2% ± 1.7% vs. 41.9% ± 2.9%, P = 0.000) and by 18% compared to the negative control cells (68.2% ± 1.7% vs. 50.0% ± 0.5%, P = 0.003). Propidium iodide and Hoechst staining indicated no significant change in the number of HEK293 cells undergoing apoptosis 6 days after pCMV6-trucated-Vegfr2 transfection, compared to the negative control. Soluble VEGFR2 produced by pCMV6-truncated-rVegfr2 inhibited full-length VEGFR2 protein expression in the cell membrane.
Conclusions
This study employed a eukaryotic system to express sVEGFR2. The use of transient transfection technology greatly improved transfect efficiency. Recombinant sVEGFR2 inhibited the effect of endogenous full-length VEGFR2 but was not cytotoxic.
doi:10.1186/2045-3701-4-14
PMCID: PMC3977943  PMID: 24618407
Gene transfection; Truncated soluble protein; Gene construction; Transient transfection
5.  Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport 
Background
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.
Results
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.
Conclusion
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.
doi:10.1186/1758-2946-5-44
PMCID: PMC3852740  PMID: 24093553
Machine vision; Cheminformatics; Virtual reality; Data mining; Optical probes; Multivariate analysis; Human-computer interaction; Graphical user interface
6.  The Subcellular Distribution of Small Molecules: from Pharmacokinetics to Synthetic Biology 
Molecular pharmaceutics  2011;8(5):1619-1628.
The systemic pharmacokinetics and pharmacodynamics of small molecules are determined by subcellular transport phenomena. Although approaches used to study the subcellular distribution of small molecules have gradually evolved over the past several decades, experimental analysis and prediction of cellular pharmacokinetics remains a challenge. In this article, we surveyed the progress of subcellular distribution research since the 1960s, with a focus on the advantages, disadvantages and limitations of the various experimental techniques. Critical review of the existing body of knowledge pointed to many opportunities to advance the rational design of organelle-targeted chemical agents. These opportunities include: 1) development of quantitative, nonfluorescence-based, whole cell methods and techniques to measure the subcellular distribution of chemical agents in multiple compartments; 2) exploratory experimentation with nonspecific transport probes that have not been enriched with putative, organelle-targeting features; 3) elaboration of hypothesis-driven, mechanistic and modeling-based approaches to guide experiments aimed at elucidating subcellular distribution and transport; and 4) introduction of revolutionary conceptual approaches borrowed from the field of synthetic biology combined with cutting edge experimental strategies. In our laboratory, state-of-the-art subcellular transport studies are now being aimed at understanding the formation of new intracellular membrane structures in response to drug therapy, exploring the function of drug-membrane complexes as intracellular drug depots, and synthesizing new organelles with extraordinary physical and chemical properties.
doi:10.1021/mp200092v
PMCID: PMC3185113  PMID: 21805990
drug transport; pharmacokinetics; biodistribution; drug targeting; databases; mathematical modeling; drug delivery; drug-membrane aggregates; unnatural organelles; synthetic organelles
7.  The Subcellular Distribution of Small Molecules: A Meta-Analysis 
Molecular pharmaceutics  2011;8(5):1611-1618.
To explore the extent to which current knowledge about the organelle-targeting features of small molecules may be applicable towards controlling the accumulation and distribution of exogenous chemical agents inside cells, molecules with known subcellular localization properties (as reported in the scientific literature) were compiled into a single data set. This data set was compared to a reference data set of approved drug molecules derived from the DrugBank database, and to a reference data set of random organic molecules derived from the PubChem database. Cheminformatic analysis revealed that molecules with reported subcellular localizations were comparably diverse. However, the calculated physicochemical properties of molecules reported to accumulate in different organelles were markedly overlapping. In relation to the reference sets of Drug Bank and Pubchem molecules, molecules with reported subcellular localizations were biased towards larger, more complex chemical structures possessing multiple ionizable functional groups and higher lipophilicity. Stratifying molecules based on molecular weight revealed that many physicochemical properties trends associated with specific organelles were reversed in smaller vs. larger molecules. Most likely, these reversed trends are due to the different transport mechanisms determining the subcellular localization of molecules of different sizes. Molecular weight can be dramatically altered by tagging molecules with fluorophores or by incorporating organelle targeting motifs. Generally, in order to better exploit structure-localization relationships, subcellular targeting strategies would benefit from analysis of the biodistribution effects resulting from variations in the size of the molecules.
doi:10.1021/mp200093z
PMCID: PMC3185174  PMID: 21774504
drug transport; pharmacokinetics; biodistribution; drug targeting; databases; mathematical modeling; drug delivery; cheminformatics
8.  Trisodium scandium bis­(orthoborate) 
Single crystals of tris­odium scandium bis­(orthoborate), Na3Sc(BO3)2, have been obtained by spontaneous crystallization from an Na2O–Sc2O3–B2O3 melt. The crystal structure features a three-dimensional framework composed of planar [BO3]3− groups and distorted ScO6 octa­hedra with Na atoms in the cavities. The Sc atom occupies a special position (Wyckoff position 2b, site symmetry -1) and of the two Na atoms, one occupies a special position (Wyckoff position 2c, site symmetry -1).
doi:10.1107/S1600536812015061
PMCID: PMC3344289  PMID: 22590055
9.  Utility of Physiologically Based Absorption Modeling in Implementing Quality by Design in Drug Development 
The AAPS Journal  2011;13(1):59-71.
To implement Quality by Design (QbD) in drug development, scientists need tools that link drug products properties to in vivo performance. Physiologically based absorption models are potentially useful tools; yet, their utility of QbD implementation has not been discussed or explored much in the literature. We simulated pharmacokinetics (PK) of carbamazepine (CBZ) after administration of four oral formulations, immediate-release (IR) suspension, IR tablet, extended-release (XR) tablet and capsule, under fasted and fed conditions and presented a general diagram of a modeling and simulation strategy integrated with pharmaceutical development. We obtained PK parameters and absorption scale factors (ASFs) by deconvolution of the PK data for IR suspension under fasted condition. The model was validated for other PK profiles of IR formulations and used to predict PK for XR formulations. We explored three key areas where a modeling and simulation approach impacts QbD. First, the model was used to help identify optimal in vitro dissolution conditions for XR formulations. Second, identification of critical formulations variables was illustrated by a parameter sensitivity analysis of mean particle radius for the IR tablet that showed a PK shift with decreased particle radius, Cmax was increased and Tmax was decreased. Finally, virtual trial simulations allowed incorporation of inter-subject variability in the model. Virtual bioequivalence studies performed for two test formulations suggested that an in vitro dissolution test may be a more sensitive discriminative method than in vivo PK studies. In summary, a well-validated predictive model is a potentially useful tool for QbD implementation in drug development.
Electronic supplementary material
The online version of this article (doi:10.1208/s12248-010-9250-9) contains supplementary material, which is available to authorized users.
doi:10.1208/s12248-010-9250-9
PMCID: PMC3032086  PMID: 21207216
advanced compartmental absorption and transit (ACAT) model; gastroplus™; modified release (MR); quality by design (QbD)
10.  Cells on Pores: A Simulation-Driven Analysis of Transcellular Small Molecule Transport 
Molecular pharmaceutics  2010;7(2):456-467.
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 3µm pore diameter membranes was more than an order of magnitude less than on 0.4µm 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.
doi:10.1021/mp9001969
PMCID: PMC2920490  PMID: 20025248
Systems Biology; Epithelial Cells; Membrane Transport; Mathematical Models; Pharmacokinetics; Cell Permeability
11.  Transcellular Transport of Heparin-coated Magnetic Iron Oxide Nanoparticles (Hep-MION) Under the Influence of an Applied Magnetic Field 
Pharmaceutics  2010;2(2):119-135.
In this study, magnetic iron oxide nanoparticles coated with heparin (Hep-MION) were synthesized and the transcellular transport of the nanoparticles across epithelial cell monolayers on porous polyester membranes was investigated. An externally applied magnetic field facilitated the transport of the Hep-MION across cell monolayers. However, high Hep-MION concentrations led to an increased aggregation of nanoparticles on the cell monolayer after application of the magnetic field. Our results indicate that magnetic guidance of Hep-MION most effectively promotes transcellular transport under conditions that minimize formation of magnetically-induced nanoparticle aggregates. Across cell monolayers, the magnet’s attraction led to the greatest increase in mass transport rate in dilute dispersions and in high serum concentrations, suggesting that magnetic guidance may be useful for in vivo targeting of Hep-MION.
doi:10.3390/pharmaceutics2020119
PMCID: PMC2997712  PMID: 21152371
magnetic iron oxide nanoparticles (MION); magnetic field; transcellular transport; MDCK cell monolayer; drug targeting
12.  Transcellular Transport of Heparin-coated Magnetic Iron Oxide Nanoparticles (Hep-MION) Under the Influence of an Applied Magnetic Field 
Pharmaceutics  2010;2(2):119-135.
In this study, magnetic iron oxide nanoparticles coated with heparin (Hep-MION) were synthesized and the transcellular transport of the nanoparticles across epithelial cell monolayers on porous polyester membranes was investigated. An externally applied magnetic field facilitated the transport of the Hep-MION across cell monolayers. However, high Hep-MION concentrations led to an increased aggregation of nanoparticles on the cell monolayer after application of the magnetic field. Our results indicate that magnetic guidance of Hep-MION most effectively promotes transcellular transport under conditions that minimize formation of magnetically-induced nanoparticle aggregates. Across cell monolayers, the magnet’s attraction led to the greatest increase in mass transport rate in dilute dispersions and in high serum concentrations, suggesting that magnetic guidance may be useful for in vivo targeting of Hep-MION.
doi:10.3390/pharmaceutics2020119
PMCID: PMC2997712  PMID: 21152371
magnetic iron oxide nanoparticles (MION); magnetic field; transcellular transport; MDCK cell monolayer; drug targeting
13.  A CELL-BASED MOLECULAR TRANSPORT SIMULATOR FOR PHARMACOKINETIC PREDICTION AND CHEMINFORMATIC EXPLORATION 
Molecular pharmaceutics  2006;3(6):704-716.
In the body, cell monolayers serve as permeability barriers, determining transport of drug molecules from one organ or tissue compartment to another. After oral administration, for example, drug 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 non-specific 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. Calculated permeability predictions showed good correlations with PAMPA, Caco2, 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.
doi:10.1021/mp060046k
PMCID: PMC2710883  PMID: 17140258
Metoprolol; permeability; chemical space; computer aided drug design; virtual screening; chemical genomics; cellular pharmacokinetics; cheminformatics; drug transport; PAMPA; Biopharmaceutics Classification System
14.  Intravitreal Triamcinolone Acetonide Inhibits Breakdown of the Blood-Retinal Barrier Through Differential Regulation of VEGF-A and Its Receptors in Early Diabetic Rat Retinas 
Diabetes  2008;57(4):1026-1033.
OBJECTIVE
To elucidate the mechanism of the unique beneficial effect of intravitreal steroid therapy on diabetic macular edema, we investigated the effect of locally administered triamcinolone acetonide (TA) on the expression of vascular endothelial growth factor (VEGF)-A and its receptors in retinas of rats with streptozotocin (STZ)-induced diabetes. We then correlated the expression of these proteins with breakdown of the blood-retinal barrier (BRB).
RESEARCH DESIGN AND METHODS
Thirty-two eyes of 16 diabetic and nondiabetic rats were divided into four groups. TA was injected into the vitreous of the right eye, and saline was injected into the left eye (control) 3.5 weeks after induction of diabetes. Retinas were harvested 48 h following treatment. mRNA and protein expression of VEGF-A, VEGF-A receptor 1 (fms-like tyrosine kinase [FLT]-1), and VEGF-A receptor 2 (fetal liver kinase [FLK]-1) were determined by real-time RT-PCR and immunohistochemistry. BRB permeability was quantitated by measuring extravasated endogenous albumin and retinal thickness.
RESULTS
Diabetes-induced retinal thickness and albumin extravasation were significantly reduced in TA-treated diabetic retinas to a level similar to that in sham-treated nondiabetic eyes. A close correlation between albumin leakage and increased expression of both Vegf-a and Flk-1 was noted in the diabetic retinas. TA downregulated the expression of Vegf-a and Flk-1 but upregulated the expression of Flt-1. TA did not alter the expression of these genes in nondiabetic retinas.
CONCLUSIONS
Intravitreal injection of TA stabilizes the BRB in association with regulation of Vegf-a, Flk-1, and Flt-1 expression in retinas in the early stages of diabetes.
doi:10.2337/db07-0982
PMCID: PMC2836241  PMID: 18174522
15.  Simulation-based cheminformatic analysis of organelle-targeted molecules: lysosomotropic monobasic amines 
Cell-based molecular transport simulations are being developed to facilitate exploratory cheminformatic analysis of virtual libraries of small drug-like molecules. For this purpose, mathematical models of single cells are built from equations capturing the transport of small molecules across membranes. In turn, physicochemical properties of small molecules can be used as input to simulate intracellular drug distribution, through time. Here, with mathematical equations and biological parameters adjusted so as to mimic a leukocyte in the blood, simulations were performed to analyze steady state, relative accumulation of small molecules in lysosomes, mitochondria, and cytosol of this target cell, in the presence of a homogenous extracellular drug concentration. Similarly, with equations and parameters set to mimic an intestinal epithelial cell, simulations were also performed to analyze steady state, relative distribution and transcellular permeability in this non-target cell, in the presence of an apical-to-basolateral concentration gradient. With a test set of ninety-nine monobasic amines gathered from the scientific literature, simulation results helped analyze relationships between the chemical diversity of these molecules and their intracellular distributions.
Electronic supplementary material
The online version of this article (doi:10.1007/s10822-008-9194-7) contains supplementary material, which is available to authorized users.
doi:10.1007/s10822-008-9194-7
PMCID: PMC2516532  PMID: 18338229
Cheminformatics; Lysosomotropic; Cellular pharmacokinetics; Drug transport; Small molecule permeability; Subcellular localization; Simulation; Rational drug design

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