GNUV201, a novel human/mouse cross-reactive and low pH-selective anti-PD-1 monoclonal antibody for cancer immunotherapy.

BACKGROUND: Several PD-1 antibodies approved as anti-cancer therapies work by blocking the interaction of PD-1 with its ligand PD-L1, thus restoring anti-cancer T cell activities. These PD-1 antibodies lack inter-species cross-reactivity, necessitating surrogate antibodies for preclinical studies, which may limit the predictability and translatability of the studies. RESULTS: To overcome this limitation, we have developed an inter-species cross-reactive PD-1 antibody, GNUV201, by utilizing an enhanced diversity mouse platform (SHINE MOUSE™). GNUV201 equally binds to human PD-1 and mouse PD-1, equally inhibits the binding of human PD-1/PD-L1 and mouse PD-1/PD-L1, and effectively suppresses tumor growth in syngeneic mouse models. The epitope of GNUV201 mapped to the "FG loop" of hPD-1, distinct from those of Keytruda® ("C'D loop") and Opdivo® (N-term). Notably, the structural feature where the protruding epitope loop fits into GNUV201's binding pocket supports the enhanced binding affinity due to slower dissociation (8.7 times slower than Keytruda®). Furthermore, GNUV201 shows a stronger binding affinity at pH 6.0 (5.6 times strong than at pH 7.4), which mimics the hypoxic and acidic tumor microenvironment (TME). This phenomenon is not observed with marketed antibodies (Keytruda®, Opdivo®), implying that GNUV201 achieves more selective binding to and better occupancy on PD-1 in the TME. CONCLUSIONS: In summary, GNUV201 exhibited enhanced affinity for PD-1 with slow dissociation and preferential binding in TME-mimicking low pH. Human/monkey/mouse inter-species cross-reactivity of GNUV201 could enable more predictable and translatable efficacy and toxicity preclinical studies. These results suggest that GNUV201 could be an ideal antibody candidate for anti-cancer drug development.

MEK1/2 inhibition rescues neurodegeneration by TFEB-mediated activation of autophagic lysosomal function in a model of Alzheimer's Disease.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder, which is characterized by cognitive deficit due to synaptic loss and neuronal death. Extracellular amyloid ß plaques are one of the pathological hallmarks of AD. The autophagic lysosomal pathway is the essential mechanism to maintain cellular homeostasis by driving clearance of protein aggregates and is dysfunctional in AD. Here, we showed that inhibiting MEK/ERK signaling using a clinically available MEK1/2 inhibitor, trametinib (GSK1120212, SNR1611), induces the protection of neurons through autophagic lysosomal activation mediated by transcription factor EB (TFEB) in a model of AD. Orally administered trametinib recovered impaired neural structures, cognitive functions, and hippocampal long-term potentiation (LTP) in 5XFAD mice. Trametinib also reduced Aß deposition via induction of autophagic lysosomal activation. RNA-sequencing analysis revealed upregulation of autophagic lysosomal genes by trametinib administration. In addition, trametinib inhibited TFEB phosphorylation at Ser142 and promoted its nuclear translocation, which in turn induced autophagic lysosomal related genes, indicating that trametinib activates the autophagic lysosomal process through TFEB activation. From these observations, we concluded that MEK inhibition provides neuronal protection from the Aß burden by increasing autophagic lysosomal activity. Thus, MEK inhibition may be an effective therapeutic strategy for AD.

Inspection of Underwater Hull Surface Condition Using the Soft Voting Ensemble of the Transfer-Learned Models.

In this study, we propose a method for inspecting the condition of hull surfaces using underwater images acquired from the camera of a remotely controlled underwater vehicle (ROUV). To this end, a soft voting ensemble classifier comprising six well-known convolutional neural network models was used. Using the transfer learning technique, the images of the hull surfaces were used to retrain the six models. The proposed method exhibited an accuracy of 98.13%, a precision of 98.73%, a recall of 97.50%, and an F1-score of 98.11% for the classification of the test set. Furthermore, the time taken for the classification of one image was verified to be approximately 56.25 ms, which is applicable to ROUVs that require real-time inspection.

Glutarate Hydroxylation by the Carbon Starvation-Induced Protein D: A Computational Study into the Stereo- and Regioselectivities of the Reaction.

The carbon starvation-induced protein D (CsiD) is a recently characterized iron(II)/α-ketoglutarate-dependent oxygenase that activates a glutarate molecule as substrate at the C2 position to exclusively produce (S)-2-hydroxyglutarate products. This selective hydroxylation reaction by CsiD is an important component of the lysine biodegradation pathway in Escherichia coli; however, little is known on the details and the origin of the selectivity of the reaction. So far, experimental studies failed to trap and characterize any short-lived catalytic cycle intermediates. As no computational studies have been reported on this enzyme either, we decided to investigate the chemical reaction mechanism of glutarate activation by an iron(IV)-oxo model of the CsiD enzyme. In this work, we present a density functional theory study on a large active site cluster model of CsiD and investigate the glutarate hydroxylation pathways by a high-valent iron(IV)-oxo species leading to (S)-2-hydroxyglutarate, (R)-2-hydroxyglutarate, and 3-hydroxyglutarate. In agreement with experimental observation, the favorable product channel leads to pro-S C2-H hydrogen atom abstraction to form (S)-2-hydroxyglutarate. The reaction is stepwise with a hydrogen atom abstraction by an iron(IV)-oxo species followed by OH rebound from a radical intermediate. The work presented in this paper shows that despite the fact that the C-H bond strengths at the C2 and C3 positions of glutarate are similar in the gas phase, substrate binding and positioning guide the reaction to an enantioselective reaction process by destabilizing the hydrogen atom abstraction pathways for the pro-R C2-H and C3-H positions. Our studies predict the chemical properties of the iron(IV)-oxo species and its rate constants with glutarate and deuterated-glutarate. Moreover, the work shows little protein motions during the catalytic process, while the substrate entrance into the substrate binding pocket appears to be guided by three active site arginine residues that position the substrate for pro-S C2-H hydrogen atom abstraction. Finally, the calculations show that irrespective of the position of the substrate and what C-H bond is closest to the metal center, the lowest energy pathway is for a selective pro-S C2-H hydrogen atom abstraction.

Druggability Assessment in TRAPP Using Machine Learning Approaches.

Accurate protein druggability predictions are important for the selection of drug targets in the early stages of drug discovery. Because of the flexible nature of proteins, the druggability of a binding pocket may vary due to conformational changes. We have therefore developed two statistical models, a logistic regression model (TRAPP-LR) and a convolutional neural network model (TRAPP-CNN), for predicting druggability and how it varies with changes in the spatial and physicochemical properties of a binding pocket. These models are integrated into TRAnsient Pockets in Proteins (TRAPP), a tool for the analysis of binding pocket variations along a protein motion trajectory. The models, which were trained on publicly available and self-augmented datasets, show equivalent or superior performance to existing methods on test sets of protein crystal structures and have sufficient sensitivity to identify potentially druggable protein conformations in trajectories from molecular dynamics simulations. Visualization of the evidence for the decisions of the models in TRAPP facilitates identification of the factors affecting the druggability of protein binding pockets.

Publisher's Note: Candidate Source of Flux Noise in SQUIDs: Adsorbed Oxygen Molecules [Phys. Rev. Lett. 115, 077002 (2015)].

This corrects the article DOI: 10.1103/PhysRevLett.115.077002.

Candidate Source of Flux Noise in SQUIDs: Adsorbed Oxygen Molecules.

A major obstacle to using superconducting quantum interference devices (SQUIDs) as qubits is flux noise. We propose that the heretofore mysterious spins producing flux noise could be O_{2} molecules adsorbed on the surface. Using density functional theory calculations, we find that an O_{2} molecule adsorbed on an α-alumina surface has a magnetic moment of ~1.8 µ_{B}. The spin is oriented perpendicular to the axis of the O-O bond, the barrier to spin rotations is about 10 mK. Monte Carlo simulations of ferromagnetically coupled, anisotropic XY spins on a square lattice find 1/f magnetization noise, consistent with flux noise in Al SQUIDs.

Role of medial prefrontal cortex Narp in the extinction of morphine conditioned place preference.

Narp knockout (KO) mice demonstrate an impaired extinction of morphine conditioned place preference (CPP). Because the medial prefrontal cortex (mPFC) has been implicated in extinction learning, we tested whether Narp cells in this region play a role in the extinction of morphine CPP. We found that intracranial injections of adenoassociated virus (AAV) expressing wild-type (WT) Narp into the mPFC of Narp KO mice rescued the extinction and the injection of AAV expressing a dominant negative form of Narp (NarpN) into the mPFC of WT mice impaired the extinction of morphine CPP. These findings suggest that Narp in the mPFC mediates the extinction of morphine CPP.

Neuronal activity-regulated pentraxin expressed in medial prefrontal cortex neurons is not necessary for extinction of heroin self-administration.

The medial prefrontal cortex (mPFC) plays a key role in extinction learning. Previously, we found that expression of a neuronal activity-regulated pentraxin (Narp) dominant-negative construct in the mPFC of mice blocked extinction of morphine-conditioned place preference. To further investigate the role of mPFC Narp in the extinction of drug seeking, we tested whether mPFC Narp is necessary for the extinction of heroin self-administration in rats. Specifically, we injected an adeno-associated viral vector expressing a dominant-negative form of Narp (NarpN) into the infralimbic region of the mPFC of rats and compared lever presses during extinction to those of rats injected with a control virus. In contrast to our previous study, we found that injection of NarpN did not affect extinction of heroin self-administration. Our findings suggest that mPFC Narp is necessary for extinction of opiate seeking in the Pavlovian-conditioned place preference paradigm but not in the operant paradigm of drug self-administration.

Trametinib activates endogenous neurogenesis and recovers neuropathology in a model of Alzheimer's disease.

Enhancing adult neurogenesis in the brain has been suggested as a potential therapeutic strategy for AD. We developed a screening platform, ATRIVIEW®, for molecules that activate neuronal differentiation of adult mouse NSCs. The most potent hit from an FDA-approved drug library was SNR1611 (trametinib), a selective MEK1/2 inhibitor. We found that trametinib increases the levels of P15INK4b and Neurog2, suggesting a mechanism by which MEK1/2 inhibition induces neuronal differentiation. Oral administration of trametinib increased adult neurogenesis in the dentate gyrus and subventricular zone of the 5XFAD AD mouse model. Surprisingly, we also found that trametinib enhanced adult neurogenesis in the cortex. Consequently, trametinib rescued AD pathologies such as neuronal loss and cognitive impairment in 5XFAD mice. Finally, trametinib induced neurogenic differentiation of NSCs derived from AD patient iPSCs, which suggests its potential therapeutic application. Altogether, we suggest that restoration of endogenous adult neurogenesis by trametinib may be a promising therapeutic approach to AD.

A receptor-targeted fluorescent radiopharmaceutical for multireporter sentinel lymph node imaging.

PURPOSE: To determine the imaging and receptor-binding properties of a multireporter probe designed for sentinel lymph node (SLN) mapping via nuclear and fluorescence detection. MATERIALS AND METHODS: The animal experiments were approved by the institutional animal care and use committee. A multireporter probe was synthesized by covalently attaching cyanine 7 (Cy7), a near-infrared cyanine dye, to tilmanocept, a radiopharmaceutical that binds to a receptor specific to recticuloendothelial cells. In vitro binding assays of technetium 99m (99mTc)-labeled Cy7 tilmanocept were conducted at 4°C by using receptor-bearing macrophages. Optical SLN imaging after foot pad administration was performed by using two molar doses of Cy7 tilmanocept. Six mice were injected with 0.11 nmol of 99mTc-labeled Cy7 tilmanocept (low-dose group); an additional six mice were injected with 31 nmol of 99mTc-labeled Cy7 tilmanocept (high-dose group) to saturate the receptor sites within the SLN. After 2.5 hours of imaging, the mice were euthanized, and the sentinel and distal lymph nodes were excised and assayed for radioactivity for calculation of SLN percentage of injected dose and extraction. Four mice were used as controls for autofluorescence. Standard optical imaging software was used to plot integrated fluorescence intensity against time for calculation of the SLN uptake rate constant and scaled peak intensity. Significance was calculated by using the Student t test. RESULTS: In vitro binding assays showed subnanomolar affinity (mean dissociation constant, 0.25 nmol/L±0.10 [standard deviation]). Fluorescence imaging showed a detection sensitivity of 1.6×10(3) counts·sec(-1)·µW(-1) per picomole of Cy7. All four imaging metrics (percentage of injected dose, SLN extraction, SLN uptake rate constant, and expected peak fluorescence intensity) exhibited higher values (P=.005 to P=.042) in the low-dose group than in the high-dose group; this finding was consistent with receptor-mediated image formation. CONCLUSION: The multireporter probe 99mTc-labeled Cy7 tilmanocept exhibits in vitro and in vivo receptor-binding properties for successful receptor-targeted SLN mapping with nuclear and optical imaging.

Dynamics of two-dimensional monolayer water confined in hydrophobic and charged environments.

We perform molecular dynamics simulations to study the effect of charged surfaces on the intermediate and long time dynamics of water in nanoconfinements. Here, we use the transferable interaction potential with five points (TIP5P) model of a water molecule confined in both hydrophobic and charged surfaces. For a single molecular layer of water between the surfaces, we find that the temperature dependence of the lateral diffusion constant of water up to very high temperatures remains Arrhenius with a high activation energy. In case of charged surfaces, however, the dynamics of water in the intermediate time regime is drastically modified presumably due to the transient coupling of dipoles of water molecules with electric field fluctuations induced by charges on the confining surfaces. Specifically, the lateral mean square displacements display a distinct super-diffusive behavior at intermediate time scale, defined as the time scale between ballistic and diffusive regimes. This change in the intermediate time-scale dynamics in the charged confinement leads to the enhancement of long-time dynamics as reflected in increasing diffusion constant. We introduce a simple model for a possible explanation of the super-diffusive behavior and find it to be in good agreement with our simulation results. Furthermore, we find that confinement and the surface polarity enhance the low frequency vibration in confinement compared to bulk water. By introducing a new effective length scale of coupling between translational and orientational motions, we find that the length scale increases with the increasing strength of the surface polarity. Further, we calculate the correlation between the diffusion constant and the excess entropy and find a disordering effect of polar surfaces on the structure of water. Finally, we find that the empirical relation between the diffusion constant and the excess entropy holds for a monolayer of water in nanoconfinement.

Localized disruption of Narp in medial prefrontal cortex blocks reinforcer devaluation performance.

Neuronal activity regulated pentraxin (Narp) is a secreted protein that regulates α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate receptors (AMPAR) aggregation and synaptogenesis. Mapping of Narp-positive neurons in brain has revealed it is prominently expressed in several limbic system projection pathways. Consistent with this localization pattern, Narp knockout mice show deficits in using the current value of a reinforcer to guide behavior, a critical function of the limbic system. To help assess whether this behavioral deficit is due to impairment of synaptogenesis during development or in modulating synaptic signaling in the mature brain, we have used a dominant negative Narp viral construct which blocks trafficking of endogenous Narp to axons. Focal injection of this viral construct into the medial prefrontal cortex (mPFC) of adult mice, a region containing Narp-positive projection neurons, blocked reinforcer devaluation. Thus, these results indicate that Narp released from mPFC neurons plays a key role in mediating synaptic changes underlying instrumental reinforcer devaluation.

Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics.

The S100A1ct peptide, consisting of the C-terminal 20 residues of the S100A1 protein fused to an N-terminal 6-residue hydrophilic tag, has been found to exert a positive inotropic effect, resulting in improved contractile performance of failing cardiac and skeletal muscle without arrhythmic side-effects. The S100A1ct peptide thus has high potential for the treatment of acute heart failure. As a step toward understanding its molecular mechanism of action, and to provide a basis for peptidomimetic design to optimize its properties, we here describe de novo structure predictions and molecular dynamics simulations to characterize the conformational landscape of S100A1ct in aqueous environment. In S100A1, the C-terminal 20 residues form an α-helix, but de novo peptide structure predictions indicate that other conformations are also possible. Conventional molecular dynamics simulations in implicit and explicit solvent corroborated this finding. To ensure adequate sampling, we performed simulations of a tagged 10-residue segment of S100A1ct, and we carried out Gaussian accelerated molecular dynamics simulations of the peptides. These simulations showed that although the helical conformation of S100A1ct was the most energetically stable, the peptide can adopt a range of kinked conformations, suggesting that its activity may be related to its ability to act as a conformational switch.

Analytical method for the fast time-domain reconstruction of fluorescent inclusions in vitro and in vivo.

A novel time-domain optical method to reconstruct the relative concentration, lifetime, and depth of a fluorescent inclusion is described. We establish an analytical method for the estimations of these parameters for a localized fluorescent object directly from the simple evaluations of continuous wave intensity, exponential decay, and temporal position of the maximum of the fluorescence temporal point-spread function. Since the more complex full inversion process is not involved, this method permits a robust and fast processing in exploring the properties of a fluorescent inclusion. This method is confirmed by in vitro and in vivo experiments.

Nicotine and Delta(9)-tetrahydrocannabinol withdrawal induce Narp in the central nucleus of the amygdala.

The central nucleus of the amygdala plays a key role in mediating aversive responses to drug withdrawal, effects thought to contribute to continued drug use. In previous studies, we found that the immediate early gene Narp, which encodes a secreted protein that binds to AMPA receptors, is induced in this nucleus following opiate withdrawal. Furthermore, Narp deletion alters the acquisition and extinction of aversive conditioning induced by opiate withdrawal. We now report that Narp is also induced in the central nucleus following withdrawal from other drugs of abuse, nicotine and Delta(9)-tetrahydrocannabinol, indicating that Narp is a common component of the transcriptional response triggered by drug withdrawal.

In vivo simultaneous monitoring of two fluorophores with lifetime contrast using a full-field time domain system.

Optical molecular imaging of small animals in vivo has witnessed dramatic growth during the past decade. Most commercial systems are based on continuous wave technology and measure solely bioluminescence or fluorescence intensity. Time domain (TD) technology enables the measurement of both intensity and fluorescence lifetime as an additional imaging metric. We have developed a novel, in-house, full-field TD system with dramatically faster acquisition times than available from a commercial TD system. Recent in vivo data from a mouse imaged with the full-field TD system has demonstrated the potential to monitor and discriminate two fluorophores injected simultaneously based on their fluorescence lifetime contrast.

Hydrogen-bond dynamics of water in a quasi-two-dimensional hydrophobic nanopore slit.

We perform molecular dynamics simulations to investigate hydrogen-bond dynamics of the TIP5P (transferable intermolecular potential with five points) model of water confined in a quasi-two-dimensional hydrophobic nanopore slit. We find that even if the average number and the lifetime of hydrogen bonds are affected by nanoconfinement, the characteristics of hydrogen-bond dynamics in hydrophobic confined water are the same as in bulk water-such as an Arrhenius temperature dependence of average hydrogen-bond lifetime and a nonexponential behavior of lifetime distributions at short time scales. The different physical properties of water in hydrophobic confinement compared to bulk water-such as approximately 40 K temperature shift-may be primarily due to the reduction of the lifetime of hydrogen bonds in confined environments. We also find that the hydrogen-bond autocorrelation function exhibits a power-law tail following a stretched exponential behavior. The relaxation time of hydrogen bonds in confined water is smaller than in bulk water. Further, we find that the temperature dependence of the relaxation time follows a power-law behavior, and the exponents for bulk and confined water are similar to each other.

Ride comfort analysis with physiological parameters for an e-health train.

Transportation by train has numerous advantages over road transportation, especially with regard to energy efficiency, ecological features, safety, and punctuality. However, the contrast in ride comfort between standard road transportation and train travel has become a competitive issue. The ride comfort enhancement technology of tilting trains (TTX) is a particularly important issue in the development of the Korean high-speed railroad business. Ride comfort is now defined in international standards such as UIC13 and ISO2631. The Korean standards such as KSR9216 mainly address physical parameters such as vibration and noise. In the area of ride comfort, living quality parameter techniques have recently been considered in Korea, Japan, and Europe. This study introduces biological parameters, particularly variations in heart rate, as a more direct measure of comfort. Biological parameters are based on physiological responses rather than on purely external mechanical parameters. Variability of heart rate and other physiological parameters of passengers are measured in a simulation involving changes in the tilting angle of the TTX. This research is a preliminary study for the implementation of an e-health train, which would provide passengers with optimized ride comfort. The e-health train would also provide feedback on altered ride comfort situations that can improve a passenger's experience and provide a healthcare service on the train. The aim of this research was to develop a ride comfort evaluation system for the railway industry, the automobile industry, and the air industry. The degree of tilt correlated with heart rate, fatigue, and unrelieved alertness.

Anionic effects on the structure and dynamics of water in superconcentrated aqueous electrolytes.

Dissolved ions in aqueous solutions are ubiquitous in a variety of systems and the addition of ions to water gives rise to dramatic effects on the properties of water. Due to a significant role of ions in the structure and dynamics of water, the ionic conditions, such as the ion type and concentration, have been considered as critical factors. Here we study the effects of anions on the structure and dynamics of water in aqueous electrolytes for various lithium salt concentrations via extensive molecular dynamics simulations. Our results demonstrate that a certain amount of salt is needed to show the different properties of water caused by the presence of different types of anion. Below the cutoff concentration, most features of water show the same characteristics in spite of the presence of different anions. In the superconcentrated limit, we find that full disruption of the hydrogen bond network between water molecules occurs for most anions investigated, indicating that the effect of the water-water interaction becomes negligible. However, a certain type of anion could enhance an ion-pairing of cations and anions and the water-water interaction remains considerable even in the superconcentrated limit. We further investigate the cationic and anionic hydration shell structures and dynamics, revealing their dependence on the anion type and the salt concentration. Finally, we observe that the anionic effects on water extend to the dynamics of water molecules, such as an anionic dependence of the onset of subdiffusive translation and anisotropic rotation.