Browsing by Subject "Kinetics"

Now showing 1 - 10 of 14
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    Development of selective inhibitors for human aldehyde dehydrogenase 3A1 (ALDH3A1) for the enhancement of cyclophosphamide cytotoxicity
    (Wiley, 2014-03) Parajuli, Bibek; Georgiadis, Taxiarchis M.; Fishel, Melissa L.; Hurley, Thomas D.; Biochemistry & Molecular Biology, School of Medicine
    Aldehyde dehydrogenase 3A1 (ALDH3A1) plays an important role in many cellular oxidative processes, including cancer chemoresistance, by metabolizing activated forms of oxazaphosphorine drugs such as cyclophosphamide (CP) and its analogues, such as mafosfamide (MF), ifosfamide (IFM), and 4-hydroperoxycyclophosphamide (4-HPCP). Compounds that can selectively target ALDH3A1 could permit delineation of its roles in these processes and could restore chemosensitivity in cancer cells that express this isoenzyme. Here we report the detailed kinetic and structural characterization of an ALDH3A1-selective inhibitor, CB29, previously identified in a high-throughput screen. Kinetic and crystallographic studies demonstrate that CB29 binds within the aldehyde substrate-binding site of ALDH3A1. Cellular proliferation of ALDH3A1-expressing lung adenocarcinoma (A549) and glioblastoma (SF767) cell lines, as well as ALDH3A1 non-expressing lung fibroblast (CCD-13Lu) cells, is unaffected by treatment with CB29 and its analogues alone. However, sensitivity toward the anti-proliferative effects of mafosfamide is enhanced by treatment with CB29 and its analogue in the tumor cells. In contrast, the sensitivity of CCD-13Lu cells toward mafosfamide was unaffected by the addition of these same compounds. CB29 is chemically distinct from the previously reported small-molecule inhibitors of ALDH isoenzymes and does not inhibit ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, or ALDH2 isoenzymes at concentrations up to 250 μM. Thus, CB29 is a novel small molecule inhibitor of ALDH3A1, which might be useful as a chemical tool to delineate the role of ALDH3A1 in numerous metabolic pathways, including sensitizing ALDH3A1-positive cancer cells to oxazaphosphorines.
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    Effects of kinetic cavity preparation vs. conventional handpiece preparation on the human dental pulp
    (1998) Collins, Julie M.; Sanders, Brian J.; Dean, Jeffrey A.; Zunt, Susan L., 1951-; El-Kafrawy, Abdel Hady, 1935-
    The purpose of this investigation was to compare the histopathologic effects of kinetic cavity preparation to the histopathologic effects of conventional high-speed handpiece preparation on the human dental pulp. The objective was to test the following hypothesis: kinetic cavity preparation results in significantly fewer pulpal effects than does conventional preparation using the high-speed handpiece. Class V cavity preparations were made in 26 teeth of seven patients who required extraction of these teeth for orthodontic purposes. Thirteen teeth were prepared using kinetic cavity preparation, using 27-um aluminum oxide particles at 160 pounds per square inch pressure. Thirteen were prepared using the high-speed handpiece and 330bur. Glass ionomer restorations were placed in all teeth. Extractions were done 10 to 15days after preparation. On teeth with closed apices, the apical one-third of the root was removed. All teeth were placed in 10 percent formalin solution. Teeth were sectioned and selected slides stained with hematoxylin and eosin for histologic evaluation. Microscopic findings indicated that the amount of remaining dentin was of significant thickness to be protective to the pulp. Pulpal responses ranged from no response in 22 specimens to a mild response in 4 specimens. Based on the results of this study, it was concluded that shallow preparation into the dentin does not cause pulpal damage at 10 to 15 days post-preparation, when using either kinetic cavity preparation or high-speed handpiece preparation. The hypothesis that kinetic cavity preparation causes significantly fewer pulpal effects than does conventional preparation with the high-speed handpiece was rejected.
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    Electrical coupling between ventricular myocytes and myofibroblasts in the infarcted mouse heart
    (European Society of Cardiology, 2018-03-01) Rubart, Michael; Tao, Wen; Lu, Xiao-Long; Conway, Simon J.; Reuter, Sean P.; Lin, Shien-Fong; Soonpaa, Mark H.; Medicine, School of Medicine
    Aims: Recent studies have demonstrated electrotonic coupling between scar tissue and the surrounding myocardium in cryoinjured hearts. However, the electrical dynamics occurring at the myocyte-nonmyocyte interface in the fibrotic heart remain undefined. Here, we sought to develop an assay to interrogate the nonmyocyte cell type contributing to heterocellular coupling and to characterize, on a cellular scale, its voltage response in the infarct border zone of living hearts. Methods and results: We used two-photon laser scanning microscopy in conjunction with a voltage-sensitive dye to record transmembrane voltage changes simultaneously from cardiomyocytes and adjoined nonmyocytes in Langendorff-perfused mouse hearts with healing myocardial infarction. Transgenic mice with cardiomyocyte-restricted expression of a green fluorescent reporter protein underwent permanent coronary artery ligation and their hearts were subjected to voltage imaging 7-10 days later. Reporter-negative cells, i.e. nonmyocytes, in the infarct border zone exhibited depolarizing transients at a 1:1 coupling ratio with action potentials recorded simultaneously from adjacent, reporter-positive ventricular myocytes. The electrotonic responses in the nonmyocytes exhibited slower rates of de- and repolarization compared to the action potential waveform of juxtaposed myocytes. Voltage imaging in infarcted hearts expressing a fluorescent reporter specifically in myofibroblasts revealed that the latter were electrically coupled to border zone myocytes. Their voltage transient properties were indistinguishable from those of nonmyocytes in hearts with cardiomyocyte-restricted reporter expression. The density of connexin43 expression at myofibroblast-cardiomyocyte junctions was ∼5% of that in the intercalated disc regions of paired ventricular myocytes in the remote, uninjured myocardium, whereas the ratio of connexin45 to connexin43 expression levels at heterocellular contacts was ∼1%. Conclusion: Myofibroblasts contribute to the population of electrically coupled nonmyocytes in the infarct border zone. The slower kinetics of myofibroblast voltage responses may reflect low electrical conductivity across heterocellular junctions, in accordance with the paucity of connexin expression at myofibroblast-cardiomyocyte contacts.
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    Modular synthesis of biologically active phosphatidic acid probes using click chemistry
    (Royal Society of Chemistry, 2009-09) Smith, Matthew D.; Sudhahar, Christopher G.; Gong, Denghuang; Stahelin, Robert V.; Best, Michael D.; Biochemistry and Molecular Biology, School of Medicine
    Phosphatidic acid (PA) is an important signaling lipid that plays roles in a range of biological processes including both physiological and pathophysiological events. PA is one of a number of signaling lipids that can act as site-specific ligands for protein receptors in binding events that enforce membrane association and generally regulate both receptor function and subcellular localization. However, elucidation of the full scope of PA activities has proven problematic, primarily due to the lack of a consensus sequence among PA-binding receptors. Thus, experimental approaches, such as those employing lipid probes, are necessary for characterizing interactions at the molecular level. Herein, we describe an efficient modular approach to the synthesis of a range of PA probes that employs a late stage introduction of reporter groups. This strategy was exploited in the synthesis of PA probes bearing fluorescent and photoaffinity tags as well as a bifunctional probe containing both a photoaffinity moiety and an azide as a secondary handle for purification purposes. To discern the ability of these PA analogs to mimic the natural lipid in protein-binding properties, each compound was incorporated into vesicles for binding studies using a known PA receptor, the C2 domain of PKCalpha. In these studies, each compound exhibited binding properties that were comparable to those of synthetic PA, indicating their viability as probes for effectively studying the activities of PA in cellular processes.
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    Molecular Recognition in a Diverse Set of Protein-Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations
    (ACS Publications, 2013-10-28) Wang, Bo; Li, Liwei; Hurley, Thomas D.; Meroueh, Samy O.; Department of Biochemistry & Molecular Biology, School of Medicine
    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal•mol−1 highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10). But larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the non-polar and entropy components, rather than a better representation of the electrostatics. SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by pre-scoring protein-ligand complexes with a machine learning-based approach (SVMSP) resulted in a significant improvement in the MM-PBSA results (ε = 1) from ρ = 0.40 to ρ = 0.81. Finally, the non-polar components of MM-GBSA and MM-PBSA, but not the electrostatic components, showed strong correlation to the ITC free energy; the computed entropies did not correlate with the ITC entropy.
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    On the reactivity of nanoparticulate elemental sulfur : experimentation and field observations
    (2017-10-02) Kafantaris, Fotios Christos; Druschel, Gregory K.; Mandernack, Kevin; Gilhooly III, William P.; Filippelli, Gabriel; Lacey, Steven E.; Toner, Brandy M.
    The reaction between elemental sulfur and sulfide is a lynchpin in the biotic and abiotic cycling of sulfur. This dissertation is focused on the reactivity of elemental sulfur nanoparticles (S8weimarn, S8raffo) among other forms of elemental sulfur (S8aq, S8aq-surfactant, α-S8), and how the variation of their surface area, character and coatings reflect on the analytical, physical-chemical and geochemical processes involving sulfur cycling. A comprehensive electrochemical investigation utilizing mercury-surface electrodes showed that elemental sulfur compounds are represented by three main voltammetric signals, corresponding to potentials at -1.2V, -0.8V, and -0.6V in the absence of organics at circumneutral pH. Dissolved S8aq-surfactant signals can be found from -0.3V up to -1.0V, depending on the surfactant in the system. Variations in current response resulted from differences in electron transfer efficiency among the forms of S8, due to their molecular structural variability. Based on this observation a new reaction pathway between S8 and Hg-surface electrodes is proposed, involving an amalgam-forming intermediate step. The kinetics of the nucleophilic dissolution of S8nano by sulfide, forming polysulfides, were investigated under varying surface area, surface character and presence or absence of surfactant coatings on S8nano. Hydrophobic S8weimarn and hydrophilic S8raffo show kinetic rate laws of 𝑟𝑆8𝑤𝑒𝑖𝑚𝑎𝑟𝑛 = 10−11.33 (𝑒 −700.65 𝑅𝑇 ) (Molar(S8)/second/dm-1) and𝑟𝑆8𝑟𝑎𝑓𝑓𝑜 = 10−4.11 𝑖−0.35 (𝑒 −615.77 𝑅𝑇 ) (Molar(S8)/second), respectively. The presence of surfactant molecules can influence the reaction pathways by dissolving S8nano and releasing S8aqsurfactant, evolving the rate-limiting step as a function of the degree of the solubilization of S8nano. The reaction rate of S8biological can be compared with those of S8raffo and S8weimarn in circumneutral pH values and T=50oC, making the forms of S8nano successful abiotic analogue models of microbially produced S8biological. Field observations and geochemical kinetic modeling in the geothermal features of Yellowstone indicate that the nucleophilic dissolution reaction appears to be a key abiotic pathway for the cycling of sulfur species and the enhancement of elemental sulfur bioavailability. Furthermore, in situ and ex situ voltammetry in the same geothermal waters disclosed chaotic variability in chemical gradients of sulfide (observed over small temporal and spatial scales) which can be considered as an ecological stressor capable of influencing single cell physiology and microbial community adaptation.
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    Population model analysis of chiral inversion and degradation of bupropion enantiomers, and application to enantiomer specific fraction unbound determination in rat plasma and brain
    (Elsevier, 2021) Bhattacharya, Chandrali; Masters, Andrea R.; Bach, Christine; Stratford, Robert E., Jr.; Medicine, School of Medicine
    Pharmacologic effects elicited by drugs most directly relate to their unbound concentrations. Measurement of binding in blood, plasma and target tissues are used to estimate these concentrations by determining the fraction of total concentration in a biological matrix that is not bound. In the case of attempting to estimate R- and S-bupropion concentrations in plasma and brain following racemic bupropion administration, reversible chiral inversion and irreversible degradation of the enantiomers were hypothesized to confound attempts at unbound fraction estimation. To address this possibility, a kinetic modeling approach was used to quantify inversion and degradation specific processes for each enantiomer from separate incubations of each enantiomer in the two matrices, and in pH 7.4 buffer, which is also used in binding experiments based on equilibrium dialysis. Modeling analyses indicated that chiral inversion kinetics were two to four-fold faster in plasma and brain than degradation, with only inversion observed in buffer. Inversion rate was faster for S-bupropion in the three media; whereas, degradation rates were similar for the two enantiomers in plasma and brain, with overall degradation in plasma approximately 2-fold higher than in brain homogenate. Incorporation of degradation and chiral inversion kinetic terms into a model to predict enantiomer-specific binding in plasma and brain revealed that, despite existence of these two processes, empirically derived estimates of fraction unbound were similar to model-derived values, leading to a firm conclusion that observed extent of plasma and brain binding are accurate largely because binding kinetics are faster than parallel degradation and chiral inversion processes.
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    Rapid Discharge of Solid-State Hydrogen Storage Using Porous Silicon and Metal Foam
    (World Academy of Science, Engineering and Technology, 2022-01-11) Potter, Loralee P.; Schubert, Peter J.; Engineering Technology, School of Engineering and Technology
    Solid-state hydrogen storage using catalytically-modified porous silicon can be rapidly charged at moderate pressures (8 bar) without exothermic runaway. Discharge requires temperatures of approximately 110oC, so for larger storage vessels a means is required for thermal energy to penetrate bulk storage media. This can be realized with low-density metal foams, such as Celmet™. This study explores several material and dimensional choices of the metal foam to produce rapid heating of bulk silicon particulates. Experiments run under vacuum and in a pressurized hydrogen environment bracket conditions of empty and full hydrogen storage vessels, respectively. Curve-fitting of the heating profiles at various distances from an external heat source is used to derive both a time delay and a characteristic time constant. System performance metrics of a hydrogen storage subsystem are derived from the experimental results. A techno-economic analysis of the silicon and metal foam provides comparison with other methods of storing hydrogen for mobile and portable applications.