Diamond, Scott L
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Publication Identification of Novel Inhibitors of Dietary Lipid Absorption using Zebrafish(2010-08-25) Clifton, Justin D; Lucumi, Edinson; Smith, Amos B; Huryn, Donna M; Myers, Michael C; Diamond, Scott L; Napper, Andrew; Pack, Michael; Hama, Kotaro; Farber, Steven APharmacological inhibition of dietary lipid absorption induces favorable changes in serum lipoprotein levels in patients that are at risk for cardiovascular disease and is considered an adjuvant or alternative treatment with HMG-CoA reductase inhibitors (statins). Here we demonstrate the feasibility of identifying novel inhibitors of intestinal lipid absorption using the zebrafish system. A pilot screen of an unbiased chemical library identified novel compounds that inhibited processing of fluorescent lipid analogues in live zebrafish larvae. Secondary assays identified those compounds suitable for testing in mammals and provided insight into mechanism of action, which for several compounds could be distinguished from ezetimibe, a drug used to inhibit cholesterol absorption in humans that broadly inhibited lipid absorption in zebrafish larvae. These findings support the utility of zebrafish screening assays to identify novel compounds that target complex physiological processes.Publication Kinetics of random aggregation-fragmentation processes with multiple components(2003-05-09) Laurenzi, Ian J.; Diamond, Scott LA computationally efficient algorithm is presented for exact simulation of the stochastic time evolution of spatially homogeneous aggregation-fragmentation processes featuring multiple components or conservation laws. The algorithm can predict the average size and composition distributions of aggregating particles as well as their fluctuations, regardless of the functional form (e.g., composition dependence) of the aggregation or fragmentation kernels. Furthermore, it accurately predicts the complete time evolutions of all moments of the size and composition distributions, even for systems that exhibit gel transitions. We demonstrate the robustness and utility of the algorithm in case studies of linear and branched polymerization processes, the last of which is a two-component process. These simulation results provide the stochastic description of these processes and give new insights into their gel transitions, fluctuations, and long-time behavior when deterministic approaches to aggregation kinetics may not be reliable.Publication Enzyme microarrays assembled by acoustic dispensing technology(2008-10-01) Wong, E. Y; Diamond, Scott LMiniaturizing bioassays to the nanoliter scale for high-throughput screening reduces the consumption of reagents that are expensive or difficult to handle. Through the use of acoustic dispensing technology, nanodroplets containing 10 μM ATP (3 μCi/μL 32P) and reaction buffer in 10% glycerol were positionally dispensed to the surface of glass slides to form 40-nL compartments (100 droplets/slide) for Pim1 (proviral integration site 1) kinase reactions. The reactions were activated by dispensing 4 nL of various levels of a pyridocarbazolo-cyclopentadienyl ruthenium complex Pim1 inhibitor, followed by dispensing 4 nL of a Pim1 kinase and peptide substrate solution to achieve final concentrations of 150 nM enzyme and 10 μM substrate. The microarray was incubated at 30 °C (97% Rh) for 1.5 h. The spots were then blotted to phosphocellulose membranes to capture phosphorylated substrate. With phosphor imaging to quantify the washed membranes, the assay showed that, for doses of inhibitor from 0.75 to 3 μM, Pim1 was increasingly inhibited. Signal-to-background ratios were as high as 165, and average coefficients of variation for the assay were not, vert, ∼20%. Coefficients of variation for dispensing typical working buffers were under 5%. Thus, microarrays assembled by acoustic dispensing are promising as cost-effective tools that can be used in protein assay development.Publication Identification and synthesis of a unique thiocarbazate cathepsin L inhibitor(2008-01-01) Myers, Michael C; Diamond, Scott L; Shah, Parag P; Smith, Amos B; Huryn, Donna MLibrary samples containing 2,5-disubstituted oxadiazoles were identified as potent hits in a high throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR) directed at discovering inhibitors of cathepsin L. However, when synthesized in pure form, the putative actives were found to be devoid of biological activity. Analyses by LC–MS of original library samples indicated the presence of a number of impurities, in addition to the oxadiazoles. Synthesis and bioassay of the probable impurities led to the identification of a thiocarbazate that likely originated via ring opening of the oxadiazole. Previously unknown, thiocarbazates (-)-11 and (-)-12 were independently synthesized as single enantiomers and found to inhibit cathepsin 20 L in the low nanomolar range.Publication Hemodynamic Regulation of Inflammation at the Endothelial-Neutrophil Interface(2008-04-01) Ji, Julie Y; Jing, Huiyan; Diamond, Scott LArterial shear stress can regulate endothelial phenotype. The potential for anti-inflammatory effects of shear stress on TNFα-activated endothelium was tested in assays of cytokine expression and neutrophil adhesion. In cultured human aortic endothelial cells (HAEC), arterial shear stress of 10 dyne/cm2 blocked by > 80% the induction by 5 ng/ml TNFα of interleukin-8 (IL-8) and IL-6 secretion (50% and 90% reduction, respectively, in the presence of nitric oxide synthase antagonism with 200 μM nitro-L-arginine methylester, L-NAME). Exposure of TNFα-stimulated HAEC to arterial shear stress for 5 hr also reduced by 60% (P &#; 0.001) the conversion of neutrophil rolling to firm arrest in a venous flow assay conducted at 1 dyne/cm2. Also, neutrophil rolling lengths at 1 dyne/cm2 were longer when TNFα-stimulated HAEC were presheared for 5 hr at arterial stresses. In experiments with a synthetic promoter that provides luciferase induction to detect cis interactions of glucocorticoid receptor (GR) and NFκB, shear stress caused a marked 40-fold induction of luciferase in TNFα-treated cells, suggesting a role for GR pathways in the anti-inflammatory actions of fluid shear stress. Hemodynamic force exerts anti-inflammatory effects on cytokine activated endothelium by attenuation of cytokine expression and neutrophil firm arrest.Publication High Throughput Screening Using Enzyme Assay Microarrays(2002-10-23) Gosalia, Dhaval N.; Diamond, Scott LWe report a new slide based microarray platform for assaying multiple enzyme activities using fluorogenic substrates. The method enables us to achieve the microfluidic requirements for rapid reaction assembly and compartmentalization. We can thus determine enzymatic activities in individually controlled reaction environments containing cofactors, inhibitors and activators. Fluorogenic substrates in glycerol were arrayed onto glass slides with reaction volumes < 5 nL and feature sizes of < 150 μm. Our method allowed rapid multiple sample deliveries onto the slide (< 3 nL/spot) with no cross contamination between array positions. It enabled us to detect the activation of the fibrinolytic and coagulation proteases namely, thrombin, plasmin, factor Xa, tPa and kallikrein in human plasma. Enzyme-substrate-inhibitor assays using ten caspases were also performed. With over 400 spots/cm2, combinatorial substrate libraries with different proteases can now be rapidly profiled. An assay to detect the dose response of a thrombin inhibitor benzamidine was performed. The inhibitor was arrayed in replicates onto selected positions on the chip. After sequential subnanoliter delivery of the reaction components, the result from the array was analyzed. The expected dose response from benzamidine was seen. A CV of 5.26% was achieved for 232 positions on the array not spiked with the inhibitor. Thus, with potentially several thousand compounds per slide, using rapid sub-nanoliter delivery of components and standard equipment, the true potential of the method is in the field of high throughput screening.Publication Identification and characterization of 3-substituted pyrazolyl esters as alternate substrates for cathepsin B: The confounding effects of DTT and cysteine in biological assays(2007-09-01) Myers, Michael C; Napper, Andrew D; Motlekar, Nuzhat; Shah, Parag P; Chiu, Chun-Hao; Beavers, Mary Pat; Diamond, Scott L; Huryn, Donna M; Smith, Amos BSubstituted pyrazole esters were identified as hits in a high throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR) to identify inhibitors of the enzyme cathepsin B. Members of this class, along with functional group analogs, were synthesized in an effort to define the structural requirements for activity. Analog characterization was hampered by the need to include a reducing agent such as dithiothreitol (DTT) or cysteine in the assay, highlighting the caution required in interpreting biological data gathered in the presence of such nucleophiles. Despite the confounding effects of DTT and cysteine, our studies demonstrate that the pyrazole 1 acts as alternate substrate for cathepsin B, rather than as an inhibitor.Publication Lattice kinetic Monte Carlo simulations of convective-diffusive systems(2009-03-05) Flamm, Matthew H; Diamond, Scott L; Sinno, TalidDiverse phenomena in physical, chemical, and biological systems exhibit significant stochasticity and therefore require appropriate simulations that incorporate noise explicitly into the dynamics. We present a lattice kinetic Monte Carlo approach to simulate the trajectories of tracer particles within a system in which both diffusive and convective transports are operational. While diffusive transport is readily accounted for in a kinetic Monte Carlo simulation, we demonstrate that the inclusion of bulk convection by simply biasing the rate of diffusion with the rate of convection creates unphysical, shocklike behavior in concentrated systems due to particle pile up. We report that elimination of shocklike behavior requires the proper passing of blocked convective rates along nearest-neighbor chains to the first available particle in the direction of flow. The resulting algorithm was validated for the Taylor–Aris dispersion in parallel plate flow and multidimensional flows. This is the first generally applicable lattice kinetic Monte Carlo simulation for convection-diffusion and will allow simulations of field-driven phenomena in which drift is present in addition to diffusion.Publication Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior(2009-03-06) Purvis, Jeremy E; Radhakrishnan, Ravi; Diamond, Scott LA defining characteristic of living cells is the ability to respond dynamically to external stimuli while maintaining homeostasis under resting conditions. Capturing both of these features in a single kinetic model is difficult because the model must be able to reproduce both behaviors using the same set of molecular components. Here, we show how combining small, well-defined steady-state networks provides an efficient means of constructing large-scale kinetic models that exhibit realistic resting and dynamic behaviors. By requiring each kinetic module to be homeostatic (at steady state under resting conditions), the method proceeds by (i) computing steady-state solutions to a system of ordinary differential equations for each module, (ii) applying principal component analysis to each set of solutions to capture the steady-state solution space of each module network, and (iii) combining optimal search directions from all modules to form a global steady-state space that is searched for accurate simulation of the time-dependent behavior of the whole system upon perturbation. Importantly, this stepwise approach retains the nonlinear rate expressions that govern each reaction in the system and enforces constraints on the range of allowable concentration states for the full-scale model. These constraints not only reduce the computational cost of fitting experimental time-series data but can also provide insight into limitations on system concentrations and architecture. To demonstrate application of the method, we show how small kinetic perturbations in a modular model of platelet P2Y(1) signaling can cause widespread compensatory effects on cellular resting states.Publication Selectin-Like Kinetics and Biomechanics Promote Rapid Platelet Adhesion in Flow: The GPIbalpha-vWF Tether Bond(2002-07-01) Doggett, Teresa A.; Girdhar, Gaurav; Lawshé, Avril; Schmidtke, David W.; Laurenzi, Ian J.; Diamond, Scott L; Diacovo, Thomas G.The ability of platelets to tether to and translocate on injured vascular endothelium relies on the interaction between the platelet glycoprotein receptor Ib α(GPIbα) and the A1 domain of von Willebrand factor (vWF-A1). To date, limited information exists on the kinetics that govern platelet interactions with vWF in hemodynamic flow. We now report that the GPIbα-vWF-A1 tether bond displays similar kinetic attributes as the selectins including: 1) the requirement for a critical level of hydrodynamic flow to initiate adhesion, 2) short-lived tethering events at sites of vascular injury in vivo, and 3) a fast intrinsic dissociation rate constant, koffo (3.45 ± 0.37 s-1). Values for koff, as determined by pause time analysis of transient capture/release events, were also found to vary exponentially (4.2 ± 0.8 s-1 to 7.3 ± 0.4 s-1) as a function of the force applied to the bond (from 36 to 217 pN). The biological importance of rapid bond dissociation in platelet adhesion is demonstrated by kinetic characterization of the A1 domain mutation, I546V that is associated with type 2B von Willebrand disease (vWD), a bleeding disorder that is due to the spontaneous binding of plasma vWF to circulating platelets. This mutation resulted in a loss of the shear threshold phenomenon, a approximately sixfold reduction in koff, but no significant alteration in the ability of the tether bond to resist shear-induced forces. Thus, flow dependent adhesion and rapid and force-dependent kinetic properties are the predominant features of the GPIbα–vWF-A1 tether bond that in part may explain the preferential binding of platelets to vWF at sites of vascular injury, the lack of spontaneous platelet aggregation in circulating blood, and a mechanism to limit thrombus formation.