Uncovering New Conformational States of the Substrate Binding Pocket of LSD1 Potential for Inhibitor Design via Funnel Metadynamics.

Lysine-specific demethylase 1 (LSD1) is a promising therapeutic target for cancer therapy. So far, over 80 crystal structures of LSD1 in different complex states have been deposited in the Protein Data Bank, which are valuable resources for performing structure-based drug design. However, among all of the crystal structures of LSD1, the substrate binding pocket, which is the most efficient druggable site for designing LSD1 inhibitors at present, is very similar no matter whether LSD1 is in the apo or any holo forms, which is inconsistent with its versatile demethylase functions. To investigate whether the substrate binding pocket is rigid or exhibits other representative conformations different from the crystal conformations that are feasible for designing new LSD1 inhibitors, we performed funnel metadynamics simulations to study the conformation dynamics of LSD1 in the binding process of two effective LSD1 inhibitors (CC-90011 and 6X0, CC-90011 undergoing clinical trials). Our results showed that the entrance of the substrate binding pocket is very flexible. Two representative entrance conformations of LSD1 counting against binding with the substrate of histone H3 were detected, which may be used for structure-based LSD1 inhibitor design. Besides, alternative optimal binding modes and prebinding modes for both inhibitors were also detected, which depicted that the key interactions changed along with the binding process. Our results should provide great help for LSD1 inhibitor design.

Improved dispersion-encoded full-range spectral interferometry for large depth, large inclination and rough samples.

In this study, we provide and validate an enhanced dispersion-encoded full-range spectral interferometry that offers improved measurement accuracy for samples characterized by significant depth, inclination, and roughness. Due to the low intensity of the optical signal in these samples, the optical signal is easy to be overwhelmed by the disturbance terms, demanding a more precise phase compensation. To address this issue, the direct current is removed by subtracting the envelope of the interference spectrum, allowing the weak signal near zero optical delay can be identified. Besides, considering the unwrapped phase error caused by the spectrometer aberrations, only the data with good phase continuity are preserved, which improves the accuracy of phase compensation. Using the proposed technique, the depth measurement range of the system is extended from 6 mm to 12 mm, while achieving an axial measurement precision of 2.5µm. In addition, the full-depth images of a ceramic standard step block and a 3D-printed sample are measured. It shows that our system exhibits superior adaptation to complex surfaces compared to the laser line profiler.

Discovery of Novel 1,3-Diphenylpyrazine Derivatives as Potent S-Phase Kinase-Associated Protein 2 (Skp2) Inhibitors for the Treatment of Cancer.

F-box protein S-phase kinase-associated protein 2 (Skp2) is a component of cullin-RING ligases, which is responsible for recruiting and ubiquitinating substrates and subsequently plays its proteolytic and non-proteolytic role. High expression of Skp2 is frequently observed in multiple aggressive tumor tissues and associated with poor prognosis. Several of the Skp2 inhibitors have been reported in the last decades; however, few of them have shown detailed structure-activity relationship (SAR) and potent bioactivity. Herein, based on the hit compound 11a from our in-house library, we optimize and synthesize a series of new 2,3-diphenylpyrazine-based inhibitors targeting the Skp2-Cks1 interaction and further systematically study the SAR. Among them, compound 14i shows potent activity against the Skp2-Cks1 interaction with an IC50 value of 2.8 µM and against PC-3 and MGC-803 cells with IC50 values of 4.8 and 7.0 µM, respectively. Most importantly, compound 14i exhibited effectively anticancer effects on PC-3 and MGC-803 xenograft mice models without obvious toxicity.

Elucidating the molecular determinants in the process of gastrin C-terminal pentapeptide amide end activating cholecystokinin 2 receptor by Gaussian accelerated molecular dynamics simulations.

Gastrin plays important role in stimulating the initiation and development of many gastrointestinal diseases through interacting with the cholecystokinin 2 receptor (CCK2R). The smallest bioactive unit of gastrin activating CCK2R is the C-terminal tetrapeptide capped with an indispensable amide end. Understanding the mechanism of this smallest bioactive unit interacting with CCK2R on a molecular basis could provide significant insights for designing CCK2R antagonists, which can be used to treat gastrin-related diseases. To this end, we performed extensive Gaussian accelerated molecular dynamics simulations to investigate the interaction between gastrin C-terminal pentapeptide capped with/without amide end and CCK2R. The amide cap influences the binding modes of the pentapeptide with CCK2R by weakening the electrostatic attractions between the C-terminus of the pentapeptide and basic residues near the extracellular domain in CCK2R. The C-terminus with the amide cap penetrates into the transmembrane domain of CCK2R while floating at the extracellular domain without the amide cap. Different binding modes induced different conformational dynamics of CCK2R. Residue pairs in CCK2R had stronger correlated motions when binding with the amidated pentapeptide. Key residues and interactions important for CCK2R binding with the amidated pentagastrin were also identified. Our results provide molecular insights into the determinants of the bioactive unit of gastrin activating CCK2R, which would be of great help for the design of CCK2R antagonists.

Bayesian reconstruction method for underwater 3D range-gated imaging enhancement.

We investigate a systematic improvement for 3D range-gated imaging in scattering environments. Drawbacks including absorption, ambient light, and scattering effect are studied. The former two are compensated through parameter estimation and preprocessing. With regard to the scattering effect, we propose a new 3D reconfiguration algorithm using a Bayesian approach that incorporates spatial constraints through a general Gaussian Markov random field. The model takes both scene depth and albedo into account, which provides a more informative and accurate restoration result. Hyper-parameters for the statistical mechanism are evaluated adaptively in the procedure and an iterated conditional mode optimization algorithm is employed to find an optimum solution. The performance of our method was assessed via conducting various experiments and the results also indicate that the proposed method is helpful for restoring the 2D image of a scene with improved visibility.

High-precision algorithms for critical angle refractive index measurement.

The critical angle method for refractive index measurement has attracted considerable attention. Precisely obtaining the critical angle is vital to the measurement process. Two advanced algorithms capable of improving the resolution of critical angle refractive index measurement systems are demonstrated. It is experimentally verified that the two algorithms improve the measurement resolution and retain linearity in the entire measurement range. The algorithm analyzes the data near the critical angle to achieve high precision, and this approach provides a notable improvement over the traditional algorithm. We perform verification experiments using liquid samples with low concentration differences, and the RI changes of these samples cannot be identified by traditional algorithms. The proposed algorithm is superior to the traditional method, which yields a resolution of less than 10-5 refractive index unit (RIU). The repeatability test shows that the uncertainty is 10-5 RIU (99.7% confidence).

Nanochannel-Based Transport in an Interfacial Memristor Can Emulate the Analog Weight Modulation of Synapses.

By exploiting novel transport phenomena such as ion selectivity at the nanoscale, it has been shown that nanochannel systems can exhibit electrically controllable conductance, suggesting their potential use in neuromorphic devices. However, several critical features of biological synapses, particularly their conductance modulation, which is both memorable and gradual, have rarely been reported in these types of systems due to the fast flow property of typical inorganic electrolytes. In this work, we demonstrate that electrically manipulating the nanochannel conductance can result in nonvolatile conductance tuning capable of mimicking the analog behavior of synapses by introducing a room-temperature ionic liquid (IL) and a KCl solution into the two ends of a nanochannel system. The gradual conductance-tuning mechanism is identified through fluorescence measurements as the voltage-induced movement of the interface between the immiscible IL and KCl solution, while the successful memorization of the conductance tuning is ascribed to the large viscosity of the IL. We applied a nanochannel-based synapse to a handwritten digit-recognition task, reaching an accuracy of 94%. These promising results provide important guidance for the future design of nanochannel-based neuromorphic devices and the manipulation of nanochannel transport for computing.

Self-referenced technology for refractive index measurement under mechanical vibration and temperature fluctuation.

A novel critical angle refractometer with self-referenced performance (SRCAR) under mechanical vibration and temperature fluctuation is presented. In a traditional CAR, mechanical vibrations and temperature fluctuations always exist and cause errors. To reduce these errors, a CAR is redesigned by introducing a reference glass with a known refractive index so that an exact calibration curve can always be determined, even though intense mechanical vibrations exist. To verify the insensitivity to these vibrations, the refractive index is monitored while the peak acceleration of the vibration is approximately 14 m/s2. The SRCAR is also used to measure a sample under different temperatures to verify the insensitivity to temperature fluctuations. Experimental measurements show that the SRCAR has the ability to lower the influences of vibrations as well as temperature fluctuations and retain a high precision of 2.5×10-4 refractive index units (RIU).

In situ measurement of seawater salinity with an optical refractometer based on total internal reflection method.

An optical refractive index sensor used for underway seawater salinity monitoring is proposed. Due to the empirical relation to salinity, refractive index measurement provides an alternative solution to obtain salinity of seawater. We developed a compact refractive index sensor based on total internal reflection (TIR) method. Through the repeatability and stability experiment and temperature correction, the performance of the sensor has been demonstrated experimentally. To evaluate the applicability of the sensor under real turbid sea conditions, field performance of the TIR sensor has been tested on an oceanographic cruise in the eastern of Yangtze Estuary in July 2017. The underway monitoring results show good correlation with the results provided by commercial CTD profiler.

Dissecting the Innate Immune Recognition of Opioid Inactive Isomer (+)-Naltrexone Derived Toll-like Receptor 4 (TLR4) Antagonists.

The opioid inactive isomer (+)-naltrexone is one of the rare Toll-like receptor 4 (TLR4) antagonists with good blood-brain barrier (BBB) permeability, which is a lead with promising potential for treating neuropathic pain and drug addiction. (+)-Naltrexone targets the lipopolysaccharides (LPS) binding pocket of myeloid differentiation protein 2 (MD-2) and blocks innate immune TLR4 signaling. However, the details of the molecular interactions of (+)-naltrexone and its derivatives with MD-2 are not fully understood, which hinders the ligand-based drug discovery. Herein, in silico and in vitro assays were performed to elucidate the innate immune recognition of the opioid inactive (+)-isomers. The results showed that the conserved LPS binding pocket of MD-2 accommodated these opioid inactive (+)-isomers. The calculated binding free energies of (+)-naltrexone and its derivatives in complex with MD-2 correlated well with their experimental binding affinities and TLR4 antagonistic activities. Hydrophobic residues in the MD-2 cavity interacted directly with these (+)-naltrexone based TLR4 antagonists and principally participated in ligand binding. Increasing the hydrophobicity of substituted group at N-17 improved its TLR4 antagonistic activity, while charged groups disfavored the binding with MD-2. Molecular dynamics (MD) simulations showed the binding of (+)-naltrexone or its derivatives to MD-2 stabilized the "collapsed" conformation of MD-2, consequently blocking the binding and signaling of TLR4. Thermodynamics and dynamic analysis showed the topology of substituted group at N-17 of (+)-naltrexone affected the binding with MD-2 and TLR4 antagonistic activity. This study provides a molecular insight into the innate immune recognition of opioid inactive (+)-isomers, which would be of great help for the development of next-generation of (+)-opioid based TLR4 antagonists.

Small-Angle X-ray Scattering Study of Protein Complexes with Tea Polyphenols.

Exploration of the structure of protein complexes, especially the change in conformation and aggregation behavior of proteins upon ligand binding, is crucial to clarify their bioactivities at the molecular level. We applied solution small-angle X-ray scattering (SAXS) to study the complex structure of bovine serum albumin (BSA) and trypsin binding with tea polyphenols, that is, catechin and epigallocatechin gallate (EGCG). We found that tea polyphenols can steadily promote the aggregation of proteins and protein complexes through their bridging effect. The numbers of proteins in the complexes and in the aggregates of complexes are extracted from SAXS intensity profiles, and their dependences as a function of the molar ratio of polyphenol to protein are discussed. EGCG has stronger capability than catechin to promote complex formation and further aggregation, and the aggregates of complexes have a denser core with a relatively smooth surface. The aggregates induced by catechin are loosely packed with a rough surface. BSA shows higher stability than trypsin in the formation of complex with a well-folded conformation. The synergistic unfolding of trypsin results in larger aggregates in the mixtures with more tea polyphenols. The binding affinity and number of tea polyphenols bound to each protein are further determined using fluorescence spectroscopy. The structure of protein complexes explored in this work is referable in the preparation of protein complex-based particles and the understanding of polyphenol-induced formation and further aggregation of protein complexes.

Construction of explicit models to correlate the structure and the inhibitory activity of aldose reductase: Flavonoids and sulfonyl-pyridazinones as inhibitors.

The correlation between binding energies and bioactivities is the core of structure-based computer-aided drug design. However, many models to address this correlation are still strongly system-dependent at current stage. We constructed two explicit models to correlate the binding energies with the inhibitory activities of flavonoids and sulfonyl-pyridazinones as inhibitors of aldose reductase. The introduction of multiple complex states comprised of protein, coenzyme, substrate, and inhibitor can remarkably improve the correlation coefficients, compared with that using single complex state. Recombination of energy terms from complex structures and molecular descriptors of inhibitors can further improve the correlation. The explicit models provide correlation coefficients of 0.90 and 0.92 for flavonoids and sulfonyl-pyridazinones, respectively. These models also steadily present the contribution from each energy term and the favorite of protein-inhibitor complex states. Meanwhile, we also observed that some inhibitors can accommodate alternative sites out of the conserved binding pocket at the presence/absence of coenzyme and substrate. It is responsible for the remarkable change in the binding energies and thus significantly influences the correlation between the structures and the inhibitory activities. Overall, this work presents a rational way to construct reliable explicit models through the combination of multiple physically accessible complex states, even though each of them only bears marginal information related to their activities.

Low-temperature solution-processed p-type vanadium oxide for perovskite solar cells.

A low-temperature solution-processed inorganic p-type contact material of vanadium oxide (VOx) was developed to fabricate planar-heterojunction perovskite solar cells. Using a solvent-assisted process, high-quality uniform and compact perovskite (CH3NH3PbI3) films were deposited on VOx coated substrates. Due to the high transmittance and quenching efficiency of VOx layers, a power conversion efficiency of over 14% was achieved.

Piezoelectric tuning of narrowband perfect plasmonic absorbers via an optomechanic cavity.

Optical antennas enable the control of light-matter interaction on the nanometer scale. Efficient on-chip electrical switching of plasmonic resonances is a crucial step toward the integration of optical antennas into practical optoelectronic circuits. We propose and numerically investigate the on-chip low-voltage linear electrical tuning of a narrowband optical antenna perfect absorber via a piezoelectric optomechanic cavity. Near unity absorption is realized by an array of gold nanostrip antennas separated from a membrane-based deformable backreflector by a small gap. A narrow linewidth of 33 nm at 2.58 µm is realized through the coupling between the plasmonic mode and photonic mode in the cavity-enhanced antenna structure. An aluminum nitride piezoelectric layer enabled efficient actuation of the backreflector and therefore changed the gap size, allowing for the tuning of the spectral absorption. The peak wavelength can be shifted linearly by 250 nm with 10 V of tuning voltage, and the tuning range is not limited by the pull-in effect. The polarization dependence of the nanostrip antenna coupled with the optomechanic cavity allows the use of our device as a voltage tunable polarization control device.

Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.

Sampling enrichment toward a target state, an analogue of the improvement of sampling efficiency (SE), is critical in both the refinement of protein structures and the generation of near-native structure ensembles for the exploration of structure-function relationships. We developed a hybrid molecular dynamics (MD)-Monte Carlo (MC) approach to enrich the sampling toward the target structures. In this approach, the higher SE is achieved by perturbing the conventional MD simulations with a MC structure-acceptance judgment, which is based on the coincidence degree of small angle x-ray scattering (SAXS) intensity profiles between the simulation structures and the target structure. We found that the hybrid simulations could significantly improve SE by making the top-ranked models much closer to the target structures both in the secondary and tertiary structures. Specifically, for the 20 mono-residue peptides, when the initial structures had the root-mean-squared deviation (RMSD) from the target structure smaller than 7 Å, the hybrid MD-MC simulations afforded, on average, 0.83 Å and 1.73 Å in RMSD closer to the target than the parallel MD simulations at 310K and 370K, respectively. Meanwhile, the average SE values are also increased by 13.2% and 15.7%. The enrichment of sampling becomes more significant when the target states are gradually detectable in the MD-MC simulations in comparison with the parallel MD simulations, and provide >200% improvement in SE. We also performed a test of the hybrid MD-MC approach in the real protein system, the results showed that the SE for 3 out of 5 real proteins are improved. Overall, this work presents an efficient way of utilizing solution SAXS to improve protein structure prediction and refinement, as well as the generation of near native structures for function annotation.

A Grouped Up-and-Down Method Used for Efficacy Comparison Between Two Different Defibrillation Waveforms.

Electrical defibrillation, which consists of delivering a therapeutic dose of the electrical current to the fibrillating heart with the aid of a defibrillator, is still the only effective way to treat life-threatening ventricular fibrillation (VF). However, the efficacy of electrical therapy for terminating VF is highly dependent on the waveform applied. When new defibrillation waveforms or techniques are developed, their efficacy needs to be accurately evaluated and compared to those in use. A common method for the comparison of defibrillation efficacy is to estimate and compare the individual defibrillation threshold (DFT) by constructing dose response curves or using an up-and-down method. Since DFT is calculated by repetitive and sequential shocks, there will be variability for each measurement and for each individual. This creates a considerable uncertainty for paired comparison. In this paper, a novel grouped up-and-down method is developed for the comparison of defibrillation efficacy between two different defibrillation waveforms or techniques. The efficacy of two commonly used biphasic defibrillation waveforms was compared in a porcine model of cardiac arrest using the developed method. Experimental results demonstrate that the proposed method is more sensitive for efficacy comparison and requires less defibrillation attempts compared with traditional DFT methods.

Measurement of the light scattering of single micrometer-sized particles captured with a microfluidic trap.

Light scattering detection of a single particle is significant to both theoretical developments and application progresses of particle scattering. In this work, a new method employing the polydimethylsiloxane microfluidic catcher with self-regulation was developed to detect the light scattering of an individual micro particle (20.42, 23.75, and 31.10 µm) in a wide angular range. This system can rapidly (<2 min) immobilize single particles without aggregations and continuously analyze its light scattering ranging from 2° to 162°. The high success ratio of the capture, good agreement with the anticipation, and moderate time and cost make this method a promising candidate in single-particle-scattering applications.

Improved time-of-flight range acquisition technique in underwater lidar experiments.

This paper presents an underwater lidar time-of-flight ranging system that combines the variable forgivable factor recursive least-squares (VFF-RLS) adaptive filter algorithm and the constant fraction discriminator (CFD) timing technology. The effectiveness of suppressing the backscattering and increasing timing accuracy is experimentally verified in the water basin under the different target distances, especially near the detection limit. The classical RLS is creatively transformed by introducing the VFF, which is highly correlated to the target echo at any distance. The improvement of the signal-to-backscatter ratio always exceeds 18.9 dB. The Monte Carlo simulation proves the applicability of the proposed method in the media of different turbidity. The influences of the selective timing methods on the walk error and time jitter are compared, and the optimum zero point of CFD is achieved by the slope analysis of leading (falling) edge in experimental target pulses.

Real part of refractive index measurement approach for absorbing liquid.

An algorithm based on use of a reflected refractometer to measure the real part of the refractive index (RI) for an absorbing liquid is presented. The absorption of liquid will blur the division between bright and dark regions on a Fresnel reflective curve. However, the reflective ratio at some incident angles that are less than the critical angle have little sensitivity to absorbability. Unlike common methods that extract RI from reflectivity in critical angle vicinity, the presented method acquires the real RI from reflective ratio at a subcritical angle. Supported by the theoretical analysis and experimental results on a reflected refractometer, we have achieved accuracy better than 3×10(-4) RIU on ink samples with absorption coefficient around 300 cm(-1). Additional tests on Alizarin yellow GG solutions prove that the subcritical algorithm is feasible and of high accuracy.

Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation.

To explore the inhibitory mechanism of catechins for digestive enzymes, we investigated the binding mode of catechins to a typical digestive enzyme-trypsin and analyzed the structure-activity relationship of catechins, using an integration of molecular docking, molecular dynamics simulation and binding free energy calculation. We found that catechins with different structures bound to a conservative pocket S1 of trypsin, which is comprised of residues 189-195, 214-220 and 225-228. In the trypsin-catechin complexes, Asp189 by forming strong hydrogen bonding, and Gln192, Trp215 and Gly216 through hydrophobic interactions, all significantly contribute to the binding of catechins. The number and the position of hydroxyl and aromatic groups, the structure of stereoisomers, and the orientation of catechins in the binding pocket S1 of trypsin all affect the binding affinity. The binding affinity is in the order of Epigallocatechin gallate (EGCG) > Epicatechin gallate (ECG) > Epicatechin (EC) > Epigallocatechin (EGC), and 2R-3R EGCG shows the strongest binding affinity out of other stereoisomers. Meanwhile, the synergic conformational changes of residues and catechins were also analyzed. These findings will be helpful in understanding the knowledge of interactions between catechins and trypsin and referable for the design of novel polyphenol based functional food and nutriceutical formulas.