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.

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.

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.

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.

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.

Structure and dynamics in the lithium solvation shell of nonaqueous electrolytes.

The solvation of a lithium ion has been of great importance to understand the structure and dynamics of electrolytes. In mixed electrolytes of cyclic and linear carbonates, the lithium solvation structure and the exchange dynamics of solvents strongly depend on the mixture ratio of solvents, providing a connection of the rigidity of the lithium solvation shell with the solvent composition in the shell. Here we study the dynamical properties of solvents in the solvation sheath of a lithium ion for various solvent mixture ratios via molecular dynamics simulations. Our results demonstrate that the exchange dynamics of solvents exhibits a non-monotonic behavior with a change in the mixture ratio, which keeps preserved on both short and long time scales. As the fraction of cyclic carbonate increases, we find that the structural properties of cyclic and linear carbonates binding to a lithium ion show different responses to a change in the fraction. Furthermore, we find that the rotational dynamics of cyclic carbonate is relatively insensitive to the mixture ratio in contrast to the rotational dynamics of linear carbonate. Our results further present that an anion shows different properties in structure and dynamics from solvents upon changing the mixture ratio of solvents.

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.

Dynamic features of water molecules in superconcentrated aqueous electrolytes.

An existence of ions dissolved in water has significant effects on bulk properties of water. Superconcentrated conditions have been recently proposed to provide a new concept of lithium ion batteries in order to overcome limitations for practical applications. In those conditions, water would undergo significant changes in structure and dynamics compared to its bulk properties. However, little is known about water in superconcentrated aqueous electrolytes. Here we study the properties of water in aqueous electrolytes with various salt concentrations via molecular dynamics simulations. We find that new dynamic features of water arise in the limit of an extremely high salt concentration. In particular, we observe a decoupled temporal character of water molecules exhibiting a subdiffusive translation and a diffusive rotation in the superconcentrated condition. Furthermore, we find that the rotational dynamics for each principal axis of a water molecule differently responds to the salt concentration, resulting in an occurrence of anisotropy in the rotation as the salt concentration increases. The superconcentrated environments also invoke new features in the hydrogen-bonding characteristics of water such as an emergence of two time scales in the hydrogen bond dynamics of water with respect to the salt concentration.

Narp Mediates Antidepressant-Like Effects of Electroconvulsive Seizures.

Growing recognition of persistent cognitive defects associated with electroconvulsive therapy (ECT), a highly effective and commonly used antidepressant treatment, has spurred interest in identifying its mechanism of action to guide development of safer treatment options. However, as repeated seizure activity elicits a bewildering array of electrophysiological and biochemical effects, this goal has remained elusive. We have examined whether deletion of Narp, an immediate early gene induced by electroconvulsive seizures (ECS), blocks its antidepressant efficacy. Based on multiple measures, we infer that Narp knockout mice undergo normal seizure activity in this paradigm, yet fail to display antidepressant-like behavioral effects of ECS. Although Narp deletion does not suppress ECS-induced proliferation in the dentate gyrus, it blocks dendritic outgrowth of immature granule cell neurons in the dentate molecular layer induced by ECS. Taken together, these findings indicate that Narp contributes to the antidepressant action of ECT and implicate the ability of ECS to induce dendritic arborization of differentiating granule cells as a relevant step in eliciting this response.

A salient effect of density on the dynamics of nonaqueous electrolytes.

The mobility and solvation of lithium ions in electrolytes are crucial for the performance and safety of lithium ion batteries. It has been known that a single type of solvent cannot satisfy the requirements of both mobility and solvation simultaneously for electrolytes. Therefore, complex solvent mixtures have been used to optimize both properties. Here we present the effects of density on the dynamics and solvation of organic liquid electrolytes via extensive molecular dynamics simulations. Our study finds that a small variation in density can induce a significant effect on the mobility of electrolytes but does not influence the solvation structure of a lithium ion. It turns out that an adjustment of the density of electrolytes could provide a more effective way to enhance mobility than a control of the solvent mixture ratio of electrolytes. Our study reveals that the density change of electrolytes mainly affects the residence time of solvents in the first solvation shell of a lithium ion rather than the structural change of the solvation sheath. Finally, our results suggest an intriguing point for understanding and designing electrolytes of lithium ion batteries for better performance and safety.

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.

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.

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.

Widom line and noise-power spectral analysis of a supercritical fluid.

We have performed extensive molecular dynamics simulations to study noise-power spectra of density and potential energy fluctuations of a Lennard-Jones model of a fluid in the supercritical region. Emanating from the liquid-vapor critical point, there is a locus of isobaric specific heat maxima, called the Widom line, which is often regarded as an extension of the liquid-vapor coexistence line. Our simulation results show that the noise-power spectrum of the density fluctuations on the Widom line of the liquid-vapor transition exhibits three distinct 1/f^{γ} behaviors with exponents γ=0, 1.2, and 2, depending on the frequency f. We find that the intermediate frequency region with an exponent γ∼ 1 appears as the temperature approaches the Widom temperature from above or below. On the other hand, we do not find three distinct regions of 1/f^{γ} in the power spectrum of the potential energy fluctuations on the Widom line. Furthermore, we find that the power spectra of both the density and potential energy fluctuations at low frequency have a maximum on the Widom line, suggesting that the noise power can provide an alternative signature of the Widom line.

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.

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.

Dynamic optical imaging of metabolic and NADPH oxidase-derived superoxide in live mouse brain using fluorescence lifetime unmixing.

Superoxide is the single-electron reduction product of molecular oxygen generated by mitochondria and the innate immune enzyme complex, nicotinamide adenine dinucleotide phosphate (NADPH) oxidase (Nox), and its isoforms. Initially identified as critical to the host defense against infection, superoxide has recently emerged as an important signaling molecule and as a proposed mediator of central nervous system injury in stroke, neurodegenerative conditions, and aging itself. Complete understanding of superoxide in central nervous system disease has been hampered by lack of noninvasive imaging techniques to evaluate this highly reactive, short-lived molecule in vivo. Here we describe a novel optical imaging technique to monitor superoxide real time in intact animals using a fluorescent probe compound and fluorescence lifetime contrast-based unmixing. Specificity for superoxide was confirmed using validated mouse models with enhanced or attenuated brain superoxide production. Application of fluorescence lifetime unmixing removed autofluorescence, further enhanced sensitivity and specificity of the technique, permitted visualization of physiologically relevant levels of superoxide, and allowed superoxide in specific brain regions (e.g., hippocampus) to be mapped. Lifetime contrast-based unmixing permitted disease model-specific and brain region-specific differences in superoxide levels to be observed, suggesting this approach may provide valuable information on the role of mitochondrial and Nox-derived superoxide in both normal function and pathologic conditions in the central nervous system.