Development of QSAR models to predict blood-brain barrier permeability.

Assessing drug permeability across the blood-brain barrier (BBB) is important when evaluating the abuse potential of new pharmaceuticals as well as developing novel therapeutics that target central nervous system disorders. One of the gold-standard in vivo methods for determining BBB permeability is rodent log BB; however, like most in vivo methods, it is time-consuming and expensive. In the present study, two statistical-based quantitative structure-activity relationship (QSAR) models were developed to predict BBB permeability of drugs based on their chemical structure. The in vivo BBB permeability data were harvested for 921 compounds from publicly available literature, non-proprietary drug approval packages, and University of Washington's Drug Interaction Database. The cross-validation performance statistics for the BBB models ranged from 82 to 85% in sensitivity and 80-83% in negative predictivity. Additionally, the performance of newly developed models was assessed using an external validation set comprised of 83 chemicals. Overall, performance of individual models ranged from 70 to 75% in sensitivity, 70-72% in negative predictivity, and 78-86% in coverage. The predictive performance was further improved to 93% in coverage by combining predictions across the two software programs. These new models can be rapidly deployed to predict blood brain barrier permeability of pharmaceutical candidates and reduce the use of experimental animals.

Strength-frequency curve for micromagnetic neurostimulation through excitatory postsynaptic potentials (EPSPs) on rat hippocampal neurons and numerical modeling of magnetic microcoil (µcoil).

Objective.The objective of this study was to measure the effect of micromagnetic stimulation (µMS) on hippocampal neurons, by using single microcoil (µcoil) prototype, magnetic pen (MagPen). MagPen will be used to stimulate the CA3 region magnetically and excitatory post synaptic potential (EPSP) response measurements will be made from the CA1 region. The threshold for micromagnetic neurostimulation as a function of stimulation frequency of the current driving theµcoil will be demonstrated. Finally, the optimal stimulation frequency of the current driving theµcoil to minimize power will be estimated.Approach.A biocompatible, watertight, non-corrosive prototype, MagPen was built, and customized such that it is easy to adjust the orientation of theµcoil and its distance over the hippocampal tissue in anin vitrorecording setting. Finite element modeling of theµcoil design was performed to estimate the spatial profiles of the magnetic flux density (in T) and the induced electric fields (in V m-1). The induced electric field profiles generated at different values of current applied to theµcoil can elicit a neuronal response, which was validated by numerical modeling. The modeling settings for theµcoil were replicated in experiments on rat hippocampal neurons.Main results.The preferred orientation of MagPen over the Schaffer Collateral fibers was demonstrated such that they elicit a neuron response. The recorded EPSPs from CA1 region due toµMS at CA3 region were validated by applying tetrodotoxin (TTX). Application of TTX to the hippocampal slice blocked the EPSPs fromµMS while after prolonged TTX washout, a partial recovery of the EPSP fromµMS was observed. Finally, it was interpreted through numerical analysis that increasing frequency of the current driving theµcoil, led to a decrease in the current amplitude threshold for micromagnetic neurostimulation.Significance.This work reports that micromagnetic neurostimulation can be used to evoke population EPSP responses in the CA1 region of the hippocampus. It demonstrates the strength-frequency curve forµMS and its unique features related to orientation dependence of theµcoils, spatial selectivity and stimulation threshold related to distance dependence. Finally, the challenges related toµMS experiments were studied including ways to overcome them.

Closed-Loop neuromodulation for clustering neuronal populations.

Pathological synchronization of neurons is associated with symptoms of movement disorders, such as Parkinson's disease and essential tremor. High-frequency deep brain stimulation (DBS) suppresses symptoms, presumably through the desynchronization of neurons. Coordinated reset (CR) delivers trains of high-frequency stimuli to different regions in the brain through multiple electrodes and may have more persistent therapeutic effects than conventional DBS. As an alternative to CR, we present a closed-loop control setup that desynchronizes neurons in brain slices by inducing clusters using a single electrode. Our setup uses calcium fluorescence imaging to extract carbachol-induced neuronal oscillations in real time. To determine the appropriate stimulation waveform for inducing clusters in a population of neurons, we calculate the phase of the neuronal populations and then estimate the phase response curve (PRC) of those populations to electrical stimulation. The phase and PRC are then fed into a control algorithm called the input of maximal instantaneous efficiency (IMIE). By using IMIE, the synchrony across the slice is decreased by dividing the population of neurons into subpopulations without suppressing the oscillations locally. The desynchronization effect is persistent 10 s after stimulation is stopped. The IMIE control algorithm may be used as a novel closed-loop DBS approach to suppress the symptoms of Parkinson's disease and essential tremor by inducing clusters with a single electrode.NEW & NOTEWORTHY Here, we present a closed-loop controller to desynchronize neurons in brain slices by inducing clusters using a single electrode using calcium imaging feedback. Phase of neurons are estimated in real time, and from the phase response curve stimulation is applied to achieve target phase differences. This method is an alternative to coordinated reset and is a novel therapy that could be used to disrupt synchronous neuronal oscillations thought to be the mechanism underlying Parkinson's disease.

Allosteric Effects of the Proton Donor on the Microbial Proton Pump Proteorhodopsin.

Proteorhodopsin (PR) is a microbial proton pump that is ubiquitous in marine environments and may play an important role in the oceanic carbon cycle. Photoisomerization of the retinal chromophore in PR leads to a series of proton transfers between specific acidic amino acid residues and the Schiff base of retinal, culminating in a proton motive force to facilitate ATP synthesis. The proton donor in a similar retinal protein, bacteriorhodopsin, acts as a latch to allow the influx of bulk water. However, it is unclear if the proton donor in PR, E108, utilizes the same latch mechanism to become internally hydrated. Here, we used molecular dynamics simulations to model the changes in internal hydration of the blue variant of PR during photoactivation with the proton donor in protonated and deprotonated states. We find that there is a stark contrast in the levels of internal hydration of the cytoplasmic half of PR based on the protonation state of E108. Instead of a latch mechanism, deprotonation of E108 acts as a gate, taking advantage of a nearby polar residue (S61) to promote the formation of a stable water wire from bulk cytoplasm to the retinal-binding pocket over hundreds of nanoseconds. No large-scale conformational changes occur in PR over the microsecond timescale. This subtle yet clear difference in the effect of deprotonation of the proton donor in PR may help explain why the photointermediates that involve the proton donor (i.e., M and N states) have timescales that are orders of magnitude different from the archaeal proton pump, bacteriorhodopsin. In general, our study highlights the importance of understanding how structural fluctuations lead to differences in the way that retinal proteins accomplish the same task.

Synchronization of heterogeneous oscillator populations in response to weak and strong coupling.

Synchronous behavior of a population of chemical oscillators is analyzed in the presence of both weak and strong coupling. In each case, we derive upper bounds on the critical coupling strength which are valid for arbitrary populations of nonlinear, heterogeneous oscillators. For weak perturbations, infinitesimal phase response curves are used to characterize the response to coupling, and graph theoretical techniques are used to predict synchronization. In the strongly perturbed case, we observe a phase dependent perturbation threshold required to elicit an immediate spike and use this behavior for our analytical predictions. Resulting upper bounds on the critical coupling strength agree well with our experimental observations and numerical simulations. Furthermore, important system parameters which determine synchronization are different in the weak and strong coupling regimes. Our results point to new strategies by which limit cycle oscillators can be studied when the applied perturbations become strong enough to immediately reset the phase.

Molecular Dynamics Simulations as a Tool for Accurate Determination of Surfactant Micelle Properties.

Molecular dynamics (MD) simulations were used to characterize the equilibrium size, shape, hydration, and self-assembly of dodecylphosphocholine (DPC) and dodecyl-ß-D-maltoside (DDM) micelles. We show that DPC molecules self-assemble to form micelles with sizes within the range reported in the experimental literature. The equilibrium shape of DPC and DDM micelles as well as associated micellar radii are in agreement with small-angle X-ray scattering (SAXS) experiments and theoretical packing parameters. In addition, we show that hydration of the micelle interior is limited; however, flexibility of the acyl chains leads to dynamic encounters with the solvated outer shell of the micelle, providing an explanation for long-standing differences in models of micelle hydration. Altogether, our results provide fundamental understanding of physical characteristics of micelles that can be utilized to study other types of detergents and proteomicelle complexes.

Desynchronization of stochastically synchronized chemical oscillators.

Experimental and theoretical studies are presented on the design of perturbations that enhance desynchronization in populations of oscillators that are synchronized by periodic entrainment. A phase reduction approach is used to determine optimal perturbation timing based upon experimentally measured phase response curves. The effectiveness of the perturbation waveforms is tested experimentally in populations of periodically and stochastically synchronized chemical oscillators. The relevance of the approach to therapeutic methods for disrupting phase coherence in groups of stochastically synchronized neuronal oscillators is discussed.