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1.  Trigger-Responsive Helical Polypeptides Capable of Toxicity Reduction and DNA Unpacking toward Non-Viral Gene Delivery 
PMCID: PMC4232450  PMID: 23832670
Non-viral gene delivery; cell penetrating peptide; helix disruption; charge conversion; photo-responsiveness
2.  Site of Death among Nursing Home Residents in the United States: Changing Patterns, 2003–2007 
The proportion of US deaths occurring in nursing homes (NHs) has been increasing in the last two decades and is expected to reach 40% by 2020. Despite being recognized as an important setting in the provision of end-of-life care (EOL), little is known about the quality of care provided to dying NH residents. There has been some, but largely anecdotal evidence suggesting that many US NHs transfer dying residents to hospitals, in part to avoid incurring the cost of providing intensive on-site care, and in part because they lack resources to appropriately serve the dying residents. We assessed longitudinal trends and geographic variations in place of death among NH residents, and examined the association between residents’ characteristics, treatment preferences, and the probability of dying in hospitals.
We used the Minimum Data Set (NH assessment records), Medicare denominator (eligibility) file, and Medicare inpatient and hospice claims to identify decedent NH residents. In CY2003–2007, there were 2,992,261 Medicare eligible nursing home decedents from 16,872 US Medicare and/or Medicaid certified NHs. Our outcome of interest was death in NH or in a hospital. The analytical strategy included descriptive analyses and multiple logistic regression models, with facility fixed effects, to examine risk-adjusted temporal trends in place of death.
Slightly over 20% of decedent NH residents died in hospitals each year. Controlling for individual level risk factors and for facility fixed effects, the likelihood of residents dying in hospitals has increased significantly each year between 2003 through 2007.
This study fills a significant gap in the current literature on EOL care in US nursing homes by identifying frequent facility-to-hospital transfers and an increasing trend of in-hospital deaths. These findings suggest a need to rethink how best to provide care to EOL nursing home residents.
PMCID: PMC3744590  PMID: 23664483
nursing homes; place of death; hospitalization
3.  Hospice Utilization in Nursing Homes: Association With Facility End-of-Life Care Practices 
The Gerontologist  2012;53(5):817-827.
Objectives: Hospice care provided to nursing home (NH) residents has been shown to improve the quality of end-of-life (EOL) care. However, hospice utilization in NHs is typically low. This study examined the relationship between facility self-reported EOL practices and residents’ hospice use and length of stay. Design: The study was based on a retrospective cohort of NH residents. Medicare hospice claims, Minimum Data Set, Online Survey, Certification, and Reporting system and the Area Resource File were linked with a survey of directors of nursing (DON) regarding institutional EOL practice patterns (EOLC Survey). Setting and Participants: In total, 4,540 long-term–care residents who died in 2007 in 290 facilities which participated in the EOLC Survey were included in this study. Measurements: We measured NHs’ tendency to offer hospice to residents and to initiate aggressive treatments (hospital transfers and feeding tubes) for EOL residents based on DON’s responses to survey items. Residents’ hospice utilization was determined using Medicare hospice claims. Results: The prevalence of hospice use was 18%. The average length of stay was 93 days. After controlling for individual risk factors, facilities’ self-reported practice measures associated with residents’ likelihood of using hospice were tendency to offer hospice (p = .048) and tendency to hospitalize (p = .002). Residents in NHs reporting higher tendency to hospitalize tended to enroll in hospice closer to death. Conclusion: Residents’ hospice utilization is not only associated with individual and facility characteristics but also with NHs’ self-reported EOL care practices. Potential interventions to effect greater use of hospice may need to focus on facility-level care processes and practices.
PMCID: PMC3858022  PMID: 23231947
Hospice utilization; Hospice length of stay; Quality of end-of-life care; Nursing home end-of-life care practices; Hospice referral
4.  End of Life Quality of Care Among Long-Term Nursing Home Decedent Residents With and Without Dementia 
To describe the longitudinal patterns and the within- and across-facility differences in hospice use and in-hospital deaths between long-term nursing home decedent residents with and without dementia.
Retrospective analyses of secondary datasets for CY2003–2007.
Nursing homes in the USA.
A total of 1,261,726 decedents in 16,347 nursing homes were included in CY2003–2007 trend analysis and 236,619 decedents in 15,098 nursing homes in CY2007 were included in the within- and across-facility analyses.
Hospice use in the last 100 days of life, and in-hospital deaths were outcome measures. Dementia was defined as having a diagnosis of Alzheimer’s disease (AD) and/or dementia other than AD, based on the Minimum Data Set (MDS) health assessments.
Overall hospice use increased from 25.6% in 2003 to 35.7% in 2007. During this time, hospice use for decedents with dementia increased from 25.1% to 36.5%, compared to an increase from 26.5% to 34.4% for decedents without dementia. The rate of in-hospital deaths remained virtually unchanged. Within the same facility, decedents with dementia were significantly more likely to use hospice (OR=1.07, 95% CI: 1.04–1.11) and less likely to die in a hospital (OR=0.76, 95% CI: 0.74–0.78). Decedents in nursing homes with higher dementia prevalence, regardless of individual dementia status, were more likely to use hospice (OR=1.67, 95% CI: 1.22–2.27).
Nursing homes appear to provide less aggressive end of life care to decedents with dementia compared to others. Although significantly more decedent residents with dementia now receive hospice care at the end of life, the quality evaluation and monitoring of hospice programs have not been systematically conducted, and additional research in this area is warranted.
PMCID: PMC4122312  PMID: 23772891
hospice; hospitalization; place of death; in-hospital deaths; dementia
5.  Definition of the To Be Named Ligament and Vertebrodural Ligament and Their Possible Effects on the Circulation of CSF 
PLoS ONE  2014;9(8):e103451.
Few studies have been conducted specifically on the dense connective tissue located in the posterior medial part of the cervical epidural space. This study was undertaken to examine the presence of this connection between the cervical dura mater and the posterior wall of spinal canal at the level of C1–C2. 30 head-neck specimens of Chinese adults were used. Gross dissection was performed on the suboccipital regions of the 20 specimens. Having been treated with the P45 plastination method, 10 specimens were sliced (9 sagittal and 1 horizontal sections). As a result, a dense fibrous band was identified in the nuchal ligament of 29 specimens (except for one horizontal section case). This fascial structure arose from the tissue of the posterior border of the nuchal ligament and then projected anteriorly and superiorly to enter the atlantoaxial interspace. It was termed as to be named ligament (TBNL). In all 30 specimens the existence of a fibrous connection was found between the posterior aspect of the cervical dura mater and the posterior wall of the spinal canal at the level of the atlas to the axis. This fibrous connection was identified as vertebrodural ligament (VDL). The VDL was mainly subdivided into three parts, and five variations of VDL were identified. These two structures, TBNL and VDL, firmly link the posterior aspect of cervical dura mater to the rear of the atlas-axis and the nuchal region. According to these findings, the authors speculated that the movements of the head and neck are likely to affect the shape of the cervical dural sleeve via the TBNL and VDL. It is hypothesized that the muscles directly associated with the cervical dural sleeve, in the suboccipital region, may work as a pump providing an important force required to move the CSF in the spinal canal.
PMCID: PMC4118883  PMID: 25084162
6.  Non-Viral Gene Delivery via Membrane-Penetrating, Mannose-Targeting Supramolecular Self-Assembled Nanocomplexes 
PMCID: PMC3757134  PMID: 23417835
Non-Viral Gene Delivery; Supramolecular Self-Assembly; Mannose Targeting; Cell Penetrating Peptides
7.  Nursing Home Work Environment and the Risk of Pressure Ulcers and Incontinence 
Health Services Research  2011;47(3 Pt 1):1179-1200.
To examine the association between nursing home (NH) work environment attributes such as teams, consistent assignment and staff cohesion, and the risk of pressure ulcers and incontinence.
Data Sources/Setting
Minimum dataset for 46,044 residents in 162 facilities in New York State, for June 2006–July 2007, and survey responses from 7,418 workers in the same facilities.
Study Design
For each individual and facility, primary and secondary data were linked. Random effects logistic models were used to develop/validate outcome measures. Generalized estimating equation models with robust standard errors and probability weights were employed to examine the association between outcomes and work environment attributes. Key independent variables were staff cohesion, percent staff in daily care teams, and percent staff with consistent assignment. Other facility factors were also included.
Principal Findings
Residents in facilities with worse staff cohesion had significantly greater odds of pressure ulcers and incontinence, compared with residents in facilities with better cohesion scores. Residents in facilities with greater penetration of self-managed teams had lower risk of pressure ulcers, but not of incontinence. Prevalence of consistent assignment was not significantly associated with the outcome measures.
NH environments and management practices influence residents’ health outcomes. These findings provide important lessons for administrators and regulators interested in promoting NH quality improvement.
PMCID: PMC3290703  PMID: 22098384
Nursing homes; health outcomes; staff cohesion; teams; consistent assignment
8.  Supramolecular self-assembled nanoparticles mediate oral delivery of therapeutic TNF-α siRNA against systemic inflammation 
PMCID: PMC3800743  PMID: 23610013
oral siRNA delivery; TNF-α; inflammation; supramolecular self-assembly; multi-function
9.  Identification of a Novel Haemophilus parasuis-Specific B Cell Epitope Using Monoclonal Antibody against the OppA Protein 
PLoS ONE  2014;9(1):e84516.
Monoclonal antibody (MAb) 1B3 against Haemophilus parasuis (H. parasuis) was generated by fusing SP2/0 murine myeloma cells and spleen cells from BALB/c mice immunized with the whole-bacterial-cell suspension of H. parasuis HS80 (serotype 5). The MAb 1B3 showed strong reactivity with 15 serotype reference strains of H. parasuis using Dot blot and Western blot analysis. Immunoprecipitation and protein spectral analysis indicated that MAb 1B3 recognized by Oligopeptide permease A (OppA) belongs to the ATP binding cassette transporter family. In addition, a linear B-cell epitope recognized by MAb 1B3 was identified by the screening of a phage-displayed 12-mer random peptide library. Sequence analysis showed that MAb 1B3 was recognized by phages-displaying peptides with the consensus motif KTPSEXR (X means variable amino acids). Its amino acid sequence matched 469KTPAEAR475 of H. parasuis OppA protein. A series of progressively truncated peptides were synthesized to define the minimal region that was required for MAb 1B3 binding. The epitope was highly conserved in OppA protein sequences from the isolated H. parasuis strains, which was confirmed by alignment analysis. Furthermore, the minimal linear epitope was highly specific among 75 different bacterial strains as shown in sequence alignments. These results indicated MAb 1B3 might be potentially used to develop serological diagnostic tools for H. parasuis.
PMCID: PMC3887010  PMID: 24416241
10.  Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport 
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.
PMCID: PMC3852740  PMID: 24093553
Machine vision; Cheminformatics; Virtual reality; Data mining; Optical probes; Multivariate analysis; Human-computer interaction; Graphical user interface
11.  Visible Light Mediated Oxidative C-N Bond Formation/Aromatization Cascade: A New Photocatalytic Entry to N-Arylindoles 
Indoles: A joint effort of light and air We have developed a mild aerobic oxidation protocol using visible light photocatalysis to synthesize structurally diverse N-arylindoles. The procedure employs 4 mol% [Ru(bpz)3](PF6)2, 18W LED light, and is performed open to the atmosphere. Readily prepared o-stryryl anilines are converted to a variety of indoles via a cascade sequence composed of oxidation of anilines, C-N bond formation, and aromatization. A 1,2-carbon shift can be also incorporated into this cascade event to further extend the substrate scope of the method. bpz = 2, 2′-Bipyrazine
PMCID: PMC3522995  PMID: 22915489
cascade; indole; photocatalysis; ruthenium; visible light
12.  Nursing Home Work Environment and the Risk of Pressure Ulcers and Incontinence 
Health Services Research  2011;47(3 Pt 1):1179-1200.
To examine the association between nursing home (NH) work environment attributes such as teams, consistent assignment and staff cohesion and the risk of pressure ulcers and incontinence.
Minimum Data Set for 46,044 residents in 162 facilities in New York State, for June 2006-July 2007, and survey responses from 7,418 workers in the same facilities.
For each individual and facility primary and secondary data were linked. Random effects logistic models were used to develop/validate outcome measures. GEE models with robust standard errors and probability weights were employed to examine the association between outcomes and work environment attributes. Key independent variables were: staff cohesion, percent staff in daily-care teams, and percent staff with consistent assignment. Other facility factors were also included.
Residents in facilities with worse staff cohesion had significantly greater odds of pressure ulcers and incontinence, compared to residents in facilities with better cohesion scores. Residents in facilities with greater penetration of self-managed teams had lower risk of pressure ulcers, but not of incontinence. Prevalence of consistent assignment was not significantly associated with the outcome measures.
NH environments and management practices influence residents' health outcomes. These findings provide important lessons for administrators and regulators interested in promoting NH quality improvement.
PMCID: PMC3290703  PMID: 22098384
nursing homes; health outcomes; staff cohesion; teams; consistent assignment
13.  Rural–Urban Differences in End-of-Life Nursing Home Care: Facility and Environmental Factors 
The Gerontologist  2012;52(3):335-344.
Purpose of the study:
This study examines urban–rural differences in end-of-life (EOL) quality of care provided to nursing home (NH) residents.
Data and Methods:
We constructed 3 risk-adjusted EOL quality measures (QMs) for long-term decedent residents: in-hospital death, hospice referral before death, and presence of severe pain. We used CY2005-2007 100% Minimum Data Set, Medicare beneficiary file, and inpatient and hospice claims. Logistic regression models were estimated to predict the probability of each outcome conditional on decedents’ risk factors. For each facility, QMs were calculated as the difference between the actual and the expected risk-adjusted outcome rates. We fit multivariate linear regression models, with fixed state effects, for each QM to assess the association with urban–rural location.
We found urban–rural differences for in-hospital death and hospice QMs, but not for pain. Compared with NHs located in urban areas, facilities in smaller towns and in isolated rural areas have significantly (p < .001) worse EOL quality for in-hospital death and hospice use. Whereas the differences in these QMs are statistically significant between facilities located in large versus small towns, they are not statistically significant between facilities located in small towns and isolated rural areas.
This study provides empirical evidence for urban–rural differences in EOL quality of care using a national sample of NHs. Identifying differences is a necessary first step toward improving care for dying NH residents and for bridging the urban–rural gap.
PMCID: PMC3342513  PMID: 22230492
Nursing homes; Quality of care; Rural & urban issues
14.  End-of-Life Quality-of-Care Measures for Nursing Homes: Place of Death and Hospice 
Journal of Palliative Medicine  2012;15(4):438-446.
The Centers for Medicare and Medicaid Services (CMS) publishes a web-based quality report card for nursing homes. The quality measures (QMs) do not assess quality of end-of-life (EOL) care, which affects a large proportion of residents. This study developed prototype EOL QMs that can be calculated from data sources available for all nursing homes nationally.
The study included approximately 1.5 million decedents residing in 16,000 nursing homes during 2003–2007, nationally. Minimum Data Set (MDS) data were linked to Medicare enrollment files, hospital claims, and hospice claims. Random effect logistic models were estimated to develop risk-adjustment models predicting two outcome measures (place of death [POD] and hospice enrollment), which were then used to construct two EOL QMs. The distributional properties of the QMs were investigated.
The QMs exhibited moderate stability over time. They were more stable in identifying quality outliers among the larger nursing homes and in identifying poor-quality outliers than high-quality outliers.
This study offers two QMs specialized to EOL care in nursing homes that can be calculated from data that are readily available and could be incorporated in the Nursing Home Compare (NHC) report card. Further work to validate the QMs is required.
PMCID: PMC3322517  PMID: 22500481
15.  Photoinduced Cleavage of N–N Bonds of Aromatic Hydrazines and Hydrazides by Visible Light 
Synthesis  2011;2011(14):2223-2236.
A photocatalytic system involving [Ru(bpyrz)3](PF6)2·2H2O, visible light, and air has been developed for cleavage of the N–N bonds of hydrazines and hydrazides. This catalytic system is generally effective for N,N-disubstituted hydrazine and hydrazide derivatives, including arylhydrazides, N-alkyl-N-arylhydrazines, and N,N-diarylhydrazines. The utility of this cleavage reaction has been demonstrated by synthesizing a variety of secondary aromatic amines.
PMCID: PMC3609041  PMID: 23543799
nitrogen–nitrogen bonds; visible light; cleavage; ruthenium; amines
16.  Applications of Human Pharmacokinetic Prediction in First-in-Human Dose Estimation 
The AAPS Journal  2012;14(2):262-281.
Quantitative estimations of first-in-human (FIH) doses are critical for phase I clinical trials in drug development. Human pharmacokinetic (PK) prediction methods have been developed to project the human clearance (CL) and bioavailability with reasonable accuracy, which facilitates estimation of a safe yet efficacious FIH dose. However, the FIH dose estimation is still very challenging and complex. The aim of this article is to review the common approaches for FIH dose estimation with an emphasis on PK-guided estimation. We discuss 5 methods for FIH dose estimation, 17 approaches for the prediction of human CL, 6 methods for the prediction of bioavailability, and 3 tools for the prediction of PK profiles. This review may serve as a practical protocol for PK- or pharmacokinetic/pharmacodynamic-guided estimation of the FIH dose.
PMCID: PMC3326168  PMID: 22407287
allometric scaling; FIH dose; in vitro–in vivo correlations; pharmacokinetics; prediction
17.  Correlation between Epilepsy and Attention Deficit Hyperactivity Disorder: A Population-Based Cohort Study 
PLoS ONE  2013;8(3):e57926.
This study presents an evaluation of the bidirectional correlation between attention deficit hyperactivity disorder (ADHD) and epilepsy using 2 cohorts from the same population database.
We used data from the Taiwan National Health Insurance Research Database to establish 2 separate cohort studies with participants <19 years old. We subdivided Cohort 1 in 2 groups: (1) 2468 patients initially diagnosed with epilepsy during the period 1999–2008, and (2) 9810 randomly selected sex- and age-matched non-epileptic controls. We subdivided Cohort 2 into 2 groups: (1) 3664 patients with newly diagnosed ADHD and (2) 14 522 sex- and age-matched non-ADHD patients. We evaluated the risk of subsequent ADHD in relationship to epilepsy and vice versa in the 2 cohorts at the end of 2008.
The ADHD incidence in Cohort 1 was 7.76 in patients with epilepsy and 3.22 in those without epilepsy (per 1000 person-years) after a median follow-up of 7–7.5 years. The adjusted hazard ratio (HR) for ADHD was 2.54 (95% CI 2.02–3.18) in the epilepsy group compared to the non-epilepsy group. In Cohort 2, the incidence of epilepsy was 3.24 in patients with ADHD and 0.78 in those without ADHD (per 1000 person-years) after a median follow-up of 3–3.5 years and an HR of 3.94 (95% CI 2.58–6.03).
This study shows a bidirectional association between ADHD and epilepsy in the 2 cohort studies. Causative factors may be common between these 2 disorders, leading to a cascade of transcriptional changes in the brain that alter behavior or cognition prior to seizures.
PMCID: PMC3590288  PMID: 23483944
18.  A Photo Touch on Amines: New Synthetic Adventures of Nitrogen Radical Cations 
Amines have been used as sacrificial electron donors to reduce photoexcited Ru(II) or Ir(III) complexes, during which they are oxidized to nitrogen radical cations. Recently, the synthetic potential of these nitrogen radical cations have caught synthetic organic chemists’ attention. They have been exploited in various transformations yielding a number of elegant methods for amine synthesis. This article highlights recent developments on nitrogen radical cation chemistry under visible-light photocatalysis.
PMCID: PMC3571698  PMID: 23419975
amines; visible light; nitrogen radical cations; ruthenium; iridium
19.  Racial Disparities in In-Hospital Death and Hospice Use Among Nursing Home Residents at the End-of-life 
Medical care  2011;49(11):992-998.
Significant racial disparities have been reported regarding nursing home residents’ use of hospital and hospice care at the end-of-life.
To examine whether the observed racial disparities in end-of-life care are due to within- or across-facility variations.
Research Design and Subjects
Cross-sectional study of 49,048 long-term-care residents (9.23% Black and 90.77% White) in 555 New York State nursing homes who died during 2005–2007. Minimum Data Set was linked with Medicare inpatient and hospice claims.
In-hospital death determined by inpatient claims and hospice use determined by hospice claims. For each outcome, risk factors were added sequentially to examine their partial effects on the racial differences. Hierarchical models were fit to test whether racial disparities are due to within- or across-facility variations.
40.33% of Blacks and 24.07% of Whites died in hospitals; 11.55% of Blacks and 17.39% of Whites used hospice. These differences are partially due to disparate use of feeding tubes, Do-Not-Resuscitate (DNR) and Do-Not-Hospitalize (DNH) orders. We find no racial disparities in in-hospital death (OR of race=0.95, CI:0.87–1.04) or hospice use (OR of race=0.90, CI:0.79–1.02) within same facilities. Living in facilities with 10% more Blacks increases the odds of in-hospital death by 22% (OR=1.22, CI:1.17–1.26) and decreases the odds of hospice use by 15% (OR=0.85, CI:0.78–0.94).
Differential use of feeding tubes, DNR and DNH orders lead to racial differences in in-hospital death and hospice use. The remaining disparities are primarily due to overall end-of-life care practices in predominately-Black facilities, not to differential hospitalization and hospice-referral patterns within facilities.
PMCID: PMC3215761  PMID: 22002648
Racial disparities; end of life care; nursing home; hospice; hospitalization
20.  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.
PMCID: PMC3185113  PMID: 21805990
drug transport; pharmacokinetics; biodistribution; drug targeting; databases; mathematical modeling; drug delivery; drug-membrane aggregates; unnatural organelles; synthetic organelles
21.  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.
PMCID: PMC3185174  PMID: 21774504
drug transport; pharmacokinetics; biodistribution; drug targeting; databases; mathematical modeling; drug delivery; cheminformatics
22.  Multiple-Targeting and Conformational Selection in the Estrogen Receptor: Computation and Experiment 
Chemical biology & drug design  2011;78(1):137-149.
Conformational selection is a primary mechanism in biomolecular recognition. The conformational ensemble may determine the ability of a drug to compete with a native ligand for a receptor target. Traditional docking procedures which use one or few protein structures are limited and may not be able to represent a complex competition among closely related protein receptors in agonist and antagonist ensembles. Here, we test a protocol aimed at selecting a drug candidate based on its ability to synergistically bind to distinct conformational states. We demonstrate, for the case of estrogen receptor α (ERα) and estrogen receptor β (ERβ), that the functional outcome of ligand binding can be inferred from its ability to simultaneously bind both ERα and ERβ in agonist and antagonist conformations as calculated docking scores. Combining a conformational selection method with an experimental reporter gene system in yeast, we propose that several phytoestrogens can be novel estrogen receptor β selective agonists. Our work proposes a computational protocol to select estrogen receptor subtype selective agonists. Compared with other models, present method gives the best prediction in ligands’ function.
PMCID: PMC3115459  PMID: 21443691
conformational ensemble; conformational selection; docking; phytoestrogen; SERMs; two-state theory
23.  Intermolecular [3+2] Cycloaddition of Cyclopropylamines with Olefins by Visible-Light Photocatalysis** 
PMCID: PMC3330129  PMID: 22109785
cycloaddition; cyclopropylamines; photochemistry; ruthenium; visible light
24.  A Cell-based Computational Modeling Approach for Developing Site-Directed Molecular Probes 
PLoS Computational Biology  2012;8(2):e1002378.
Modeling the local absorption and retention patterns of membrane-permeant small molecules in a cellular context could facilitate development of site-directed chemical agents for bioimaging or therapeutic applications. Here, we present an integrative approach to this problem, combining in silico computational models, in vitro cell based assays and in vivo biodistribution studies. To target small molecule probes to the epithelial cells of the upper airways, a multiscale computational model of the lung was first used as a screening tool, in silico. Following virtual screening, cell monolayers differentiated on microfabricated pore arrays and multilayer cultures of primary human bronchial epithelial cells differentiated in an air-liquid interface were used to test the local absorption and intracellular retention patterns of selected probes, in vitro. Lastly, experiments involving visualization of bioimaging probe distribution in the lungs after local and systemic administration were used to test the relevance of computational models and cell-based assays, in vivo. The results of in vivo experiments were consistent with the results of in silico simulations, indicating that mitochondrial accumulation of membrane permeant, hydrophilic cations can be used to maximize local exposure and retention, specifically in the upper airways after intratracheal administration.
Author Summary
We have developed an integrative, cell-based modeling approach to facilitate the design and discovery of chemical agents directed to specific sites of action within a living organism. Here, a computational, multiscale transport model of the lung was adapted to enable virtual screening of small molecules targeting the epithelial cells of the upper airways. In turn, the transport behaviors of selected candidate probes were evaluated to establish their degree of retention at a site of absorption, using computational simulations as well as two in vitro cell-based assay systems. Lastly, bioimaging experiments were performed to examine candidate molecules' distribution in the lungs of mice after local and systemic administration. Based on computational simulations, the higher mitochondrial density per unit absorption surface area is the key parameter determining the higher retention of small molecule hydrophilic cations in the upper airways, relative to lipophilic weak bases, specifically after intratracheal administration.
PMCID: PMC3285574  PMID: 22383866
25.  Prolonged post-inhibitory rebound firing in the cerebellar nuclei mediated by group I mGluR potentiation of L-type Ca currents 
Neurons in the cerebellar nuclei fire at accelerated rates for prolonged periods after trains of synaptic inhibition that interrupt spontaneous firing. Both in vitro and in vivo, however, this prolonged rebound firing is favored by strong stimulation of afferents, suggesting that neurotransmitters other than GABA may contribute to the increased firing rates. Here, we tested whether metabotropic glutamate receptors modulate excitability of nuclear cells in cerebellar slices from mouse. In current clamp, the prolonged rebound firing rate after high-frequency synaptic stimulation was reduced by a variety of group I mGluR antagonists, including CPCCOEt (7-(hydroxyimino)cyclopropa[b]chromen-1a-carboxylate ethyl ester), JNJ16259685 ((3,4-dihydro-2H-pyrano[2,3-b]quinolin-7-yl)-(cis-4-methoxycyclohexyl)-methanone)+MPEP, or 3-MATIDA (α-amino-5-carboxy-3-methyl-2-thiopheneacetic acid) +MPEP, as long as both mGluR1 and mGluR5 were blocked. This mGluR-dependent acceleration of firing was reduced but still evident when IPSPs were prevented by GABAA receptor antagonists. In voltage clamp, voltage ramps revealed a non-inactivating, low-voltage-activated, nimodipine-sensitive current that was enhanced by the selective group I mGluR agonist s-DHPG ((S)-3,5-dihydroxyphenylglycine). This putative L-type current also increased when mGluRs were activated by trains of evoked synaptic currents instead of direct application of agonist. In current clamp, blocking L-type Ca channels with the specific blocker nifedipine greatly reduced prolonged post-stimulus firing and occluded the effect of adding group I mGluR antagonists. Thus, potentiation of a low-voltage-activated L-type current by synaptically released glutamate accounted nearly fully for the mGluR-dependent acceleration of firing. Together, these data suggest that prolonged rebound firing in the cerebellar nuclei in vivo is most likely to occur when GABAA and mGluRs are simultaneously activated by concurrent excitation and inhibition.
PMCID: PMC3155995  PMID: 21753005

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