Ku70 Binding to YAP Alters PARP1 Ubiquitination to Regulate Genome Stability and Tumorigenesis.

YAP is a central player in cancer development with functions extending beyond its recognized role in cell growth regulation. Recent work has identified a link between YAP/TAZ and the DNA damage response. Here, we investigated the mechanistic underpinnings of the crosstalk between DNA damage repair and YAP activity. Ku70, a key component of the non-homologous end joining pathway to repair DNA damage, engaged in a dynamic competition with TEAD4 for binding to YAP, limiting the transcriptional activity of YAP. Depletion of Ku70 enhanced interaction between YAP and TEAD4 and boosted YAP transcriptional capacity. Consequently, Ku70 loss enhanced tumorigenesis in colon cancer and hepatocellular carcinoma (HCC) in vivo. YAP impeded DNA damage repair and elevated genome instability by inducing PARP1 degradation through the SMURF2-mediated ubiquitin-proteasome pathway. Analysis of HCC patient samples substantiated the link between Ku70 expression, YAP activity, PARP1 levels, and genome instability. In conclusion, this research provides insight into the mechanistic interactions between YAP and key regulators of DNA damage repair, highlighting the role of a Ku70-YAP-PARP1 axis in preserving genome stability.

HTR+: a novel algorithm for identifying type and polycrystal of gas hydrates.

In this work, the hierarchical topology ring (HTR+) algorithm, an extension of the HTR algorithm, was developed for identifying gas hydrate types, cage structures, and grain boundaries (GBs) within polycrystalline structures. Utilizing molecular dynamics trajectories of polycrystalline hydrates, the accuracy of the HTR+ algorithm is validated in identifying sI, sII and sH hydrate types, hydrate grains, and GBs in multi-hydrate polycrystals, as well as clathrate cages at GBs. Additionally, during the hydrate nucleation and growth processes, clathrate cages, hydrate type, hydrate grains and ice structures are accurately recognized. Significantly, this algorithm demonstrates high efficiency, particularly for large hydrate systems. HTR+ algorithm emerges a powerful tool for identifying micro/mesoscopic structures of gas hydrates, enabling an in-depth understanding of the formation mechanisms and properties of gas hydrates.

Synthesis and structure-activity optimization of azepane-containing derivatives as PTPN2/PTPN1 inhibitors.

Protein tyrosine phosphatases PTPN2 and PTPN1 (also known as PTP1B) have been implicated in a number of intracellular signaling pathways of immune cells. The inhibition of PTPN2 and PTPN1 has emerged as an attractive approach to sensitize T cell anti-tumor immunity. Two small molecule inhibitors have been entered the clinic. Here we report the design and development of compound 4, a novel small molecule PTPN2/N1 inhibitor demonstrating nanomolar inhibitory potency, good in vivo oral bioavailability, and robust in vivo antitumor efficacy.

Precise Control of Metal Active Sites of Metal-Organic Framework Nanozymes for Achieving Excellent Enzyme-Like Activity and Efficient Pancreatitis Therapy.

Acute pancreatitis (AP) is a potentially life-threatening inflammatory disease that can lead to the development of systemic inflammatory response syndrome and its progression to severe acute pancreatitis. Hence, there is an urgent need for the rational design of highly efficient antioxidants to treat AP. Herein, an optimized Cu-based metal-organic framework (MOF) nanozyme with exceptional antioxidant activity is introduced, designed to effectively alleviate AP, by engineering the metal coordination centers in MN2Cl2 (M = Co, Ni, Cu). Specifically, the Cu MOF, which benefits from a Cu active center similar to that of natural superoxide dismutase (SOD), exhibited at least four times higher SOD-like activity than the Ni/Co MOF. Theoretical analyses further demonstrate that the CuN2Cl2 site not only has a moderate adsorption effect on the substrate molecule •OOH but also reduces the dissociation energy of the product H2 O2 . Additionally, the Cu MOF nanozyme possesses the excellent catalase-like activity and •OH removal ability. Consequently, the Cu MOF with broad-spectrum antioxidant activity can efficiently scavenge reactive oxygen species to alleviate arginine-induced AP. More importantly, it can also mitigate apoptosis and necrosis of acinar cells by activating the PINK1/PARK2-mediated mitophagy pathway. This study highlights the distinctive functions of tunable MOF nanozymes and their potential bio-applications.

Insights into the mechanical stability of tetrahydrofuran hydrates from experimental, machine learning, and molecular dynamics perspectives.

Natural gas hydrates (NGHs) hold immense potential as a future energy resource and for sustainable applications such as gas capture and storage. Due to the challenging formation conditions, however, their mechanical properties remain poorly understood. Herein, the mechanical characteristics of tetrahydrofuran (THF) hydrates, a proxy for methane hydrates, were investigated at different ice contents, strain rates, and temperatures using uniaxial compressive experiments. The results unveil a distinct behavior in the peak strength of THF hydrates with a varying ice content, strain rate and temperature, exhibiting an increase as the strain rate and temperature decrease, in contrast to the peak strength-strain rate relationship observed in polycrystalline ice. Based on the experimental data, four machine learning (ML) models including extreme gradient boosting (XGboost), multilayer perceptron (MLP), gradient boosting decision tree (GBDT) and decision tree (DT) were developed to predict the peak strength. The XGboost model demonstrates superior predictive performance, emphasizing the significant influence of ice content and temperature on the peak strength of hydrates. Furthermore, molecular dynamics (MD) simulations were employed to gain insights into the dissociation and formation processes of clathrate cages, as well as phase transitions and amorphization occurring at grain boundaries (GBs) involving diverse unconventional clathrate cages, including 51265, 4151062, 4151064, 425861 and 425862, with 425861 and 425862 cages being predominant. This study enhances our understanding of the mechanical properties and deformation mechanisms of hydrates and provides a ML-based predictive framework for estimating the compressive strength of hydrates under diverse coupling conditions. The findings have significant implications for stability assessments of NGHs and the exploitation of NGH resources.

Linear Calcium Carbonate Chains by Directional Control of Ionic Bonding.

As a result of the non-directionality of ionic bonds, oppositely charged ions always assemble into closely packed clusters or crystals rather than linear structured ionic species. Here, we generated a series of linear calcium carbonate chains, (Ca2+CO32-)n, with an orientated directionality of the ionic interactions. The formation of these ionic chains with long-range ordered ionic interactions was originally induced by the dipole orientation of the ions and subsequently preserved by capping agents. According to the appropriately established folding-capping model, rational control of the capping effect can regulate the length of the (Ca2+CO32-)n chain within 100 nm, corresponding to n ≤ 250. Our discovery overturns the current understanding of ionic bonding in chemistry and opens a way to control the assembly of inorganic ions at molecular scale, pushing forward a fusion of molecular compounds and ionic compounds that share similar topological control.

Using Cu-Based Metal-Organic Framework as a Comprehensive and Powerful Antioxidant Nanozyme for Efficient Osteoarthritis Treatment.

Developing nanozymes with effective reactive oxygen species (ROS) scavenging ability is a promising approach for osteoarthritis (OA) treatment. Nonetheless, numerous nanozymes lie in their relatively low antioxidant activity. In certain circumstances, some of these nanozymes may even instigate ROS production to cause side effects. To address these challenges, a copper-based metal-organic framework (Cu MOF) nanozyme is designed and applied for OA treatment. Cu MOF exhibits comprehensive and powerful activities (i.e., SOD-like, CAT-like, and •OH scavenging activities) while negligible pro-oxidant activities (POD- and OXD-like activities). Collectively, Cu MOF nanozyme is more effective at scavenging various types of ROS than other Cu-based antioxidants, such as commercial CuO and Cu single-atom nanozyme. Density functional theory calculations also confirm the origin of its outstanding enzyme-like activities. In vitro and in vivo results demonstrate that Cu MOF nanozyme exhibits an excellent ability to decrease intracellular ROS levels and relieve hypoxic microenvironment of synovial macrophages. As a result, Cu MOF nanozyme can modulate the polarization of macrophages from pro-inflammatory M1 to anti-inflammatory M2 subtype, and inhibit the degradation of cartilage matrix for efficient OA treatment. The excellent biocompatibility and protective properties of Cu MOF nanozyme make it a valuable asset in treating ROS-related ailments beyond OA.

ACT001 improved cardiovascular function in septic mice by inhibiting the production of proinflammatory cytokines and the expression of JAK-STAT signaling pathway.

Sepsis is a life-threatening multiple organ dysfunction syndrome (MODS) caused by a microbial infection that leads to high morbidity and mortality worldwide. Sepsis-induced cardiomyopathy (SIC) and coagulopathy promote the progression of adverse outcomes in sepsis. Here, we reported that ACT001, a modified compound of parthenolide, improved the survival of sepsis mice. In this work, we used cecal ligation and puncture (CLP) model to induce SIC. Transthoracic echocardiography and HE staining assays were adopted to evaluate the influence of ACT001 on sepsis-induced cardiac dysfunction. Our results showed that ACT001 significantly improved heart function and reduced SIC. Coagulation accelerates organ damage in sepsis. We found that ACT001 decreased blood clotting in the FeCl3-induced carotid artery thrombosis experiment. ACT001 also reduced the production of neutrophil extracellular traps (NETs). RNA-sequencing of heart tissues revealed that ACT001 significantly downregulated the expression of pro-inflammatory cytokines and the JAK-STAT signaling pathway. These results were confirmed with real-time PCR and ELISA. In summary, we found ACT001 rescued mice from septic shock by protecting the cardiovascular system. This was partially mediated by inhibiting pro-inflammatory cytokine production and down-regulating the JAK-STAT signaling.

Large-scale and cost-efficient agrivoltaics system by spectral separation.

Agrivoltaics (AV) offers a promising solution to address both food and energy crises. However, crop growth under photovoltaic (PV) conditions faces substantial challenges due to insufficient light transmission. We propose a large-scale and cost-effective spectral separated concentrated agricultural photovoltaic (SCAPV) system. The system utilizes concentrator modules, cell components, and dual-axis tracking systems to enhance power conversion efficiency (PCE), achieving a maximum PCE of 11.6%. After three years of successful operation, a 10 kWp power plant achieved an average annual electricity generation exceeding 107 MWh/ha. The results showed higher yields of various crops, including ginger and sweet potatoes, and significant improvements in soil moisture retention compared to open air. The improvements in PCE and microclimate validate the scalability of the SCAPV, which provides better plant conditions and cost-effectiveness, with an estimated cost reduction of 18.8% compared to conventional PV power plant. This study provides valuable insights and directions for improvement in AV.

Discovery of 4,5,6,7-Tetrahydropyrazolo[1.5-a]pyrizine Derivatives as Core Protein Allosteric Modulators (CpAMs) for the Inhibition of Hepatitis B Virus.

Hepatitis B Virus (HBV) core protein allosteric modulators (CpAMs) are an attractive class of potential anti-HBV therapeutic agents. Here we describe the efforts toward the discovery of a series of 4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazine (THPP) compounds as HBV CpAMs that effectively inhibit a broad range of nucleos(t)ide-resistant HBV variants. The lead compound 45 demonstrated inhibition of HBV DNA viral load in a HBV AAV mouse model by oral administration.

Selective Chiral Recognition between Amino Acids and Growing Gypsum Crystals.

In nature, selective chiral interactions between biomolecules and minerals provide insight into the mysterious origin of homochirality. Here, we show growing gypsum crystals in a nonequilibrium state can recognize chiral enantiomers of amino acids. The chiral selection for amino acids with different functional groups by growing minerals are distinct. For 11 amino acids, the d-isomer slows dynamic gypsum growth more than the l-isomer, whereas for another 7 amino acids, the opposite was observed. These differences in chiral recognition are attributed to the different stereochemical matching between the chiral amino acids and the dynamic steps of growing gypsum. These stereoselective interactions between amino acid enantiomers and dynamic growing crystals can be applied toward the fabrication of gypsum cements to regulate their structure and mechanical properties. These findings provide insight into understanding the mechanism of the origin of homochirality in nature and suggest a pathway for constructing advanced functional materials.

Thermal conductivity of fivefold twinned silicon-germanium heteronanowires.

The thermal transport properties of five-fold twinned (5FT) germanium-silicon (Ge-Si) heteronanowires (h-NWs) with varying cross-sectional areas, germanium (Ge) domain ratios and heterostructural patterns are investigated using homogeneous nonequilibrium molecular dynamics (HNEMD) simulations. The results demonstrate a distinctive behavior in the thermal conductivity (κ) of 5FT-NWs, characterized by a "flipped" trend at a critical cross-sectional area. This behavior is attributed to the hydrodynamic phonon flow, arising from the normal three-phonon scattering process in the low-frequency region. In addition, the composition ratio of 5FT-NWs has a significant impact on reducing the κ of 5FT-NWs and suppressing the hydrodynamic effect. Intriguingly, as the homogeneous element domains are separated, stronger phonon hydrodynamic flows are observed in comparison to the adjacent homogeneous element domains. By analyzing various phonon properties, including phonon dispersion, three-phonon scattering rate, and phonon mean free path, critical insights into the origin of the differential κ in different 5FT-NW structures are provided. The findings deepen the understanding of the thermal transport properties of nanomaterials and hold implications for the design and development of nanoelectronics and thermoelectric devices.

Predicting mechanical properties of CO2hydrates: machine learning insights from molecular dynamics simulations.

Understanding the mechanical properties of CO2hydrate is crucial for its diverse sustainable applications such as CO2geostorage and natural gas hydrate mining. In this work, classic molecular dynamics (MD) simulations are employed to explore the mechanical characteristics of CO2hydrate with varying occupancy rates and occupancy distributions of guest molecules. It is revealed that the mechanical properties, including maximum stress, critical strain, and Young's modulus, are not only affected by the cage occupancy rate in both large 51262and small 512cages, but also by the distribution of guest molecules within the cages. Specifically, the presence of vacancies in the 51262large cages significantly impacts the overall mechanical stability compared to 512small cages. Furthermore, four distinct machine learning (ML) models trained using MD results are developed to predict the mechanical properties of CO2hydrate with different cage occupancy rates and cage occupancy distributions. Through analyzing ML results, as-developed ML models highlight the importance of the distribution of guest molecules within the cages, as crucial contributor to the overall mechanical stability of CO2hydrate. This study contributes new knowledge to the field by providing insights into the mechanical properties of CO2hydrates and their dependence on cage occupancy rates and cage occupancy distributions. The findings have implications for the sustainable applications of CO2hydrate, and as-developed ML models offer a practical framework for predicting the mechanical properties of CO2hydrate in different scenarios.

Electric field as a crystallization switch of heterogeneous ice formation.

Using molecular dynamics simulations, we investigated the effect of external electric field on ice formation with the present of a substrate surface. It turns out that the electric field can affect the ice formation on substrate surface by altering the dipole orientation of interfacial water molecules (IWs): a crossover from inhibiting to promoting ice formation with the increase of electric field strength. According to the influence of the electric field on ice formation, the electric field strength range of 0.0 V nm-1-7.0 V nm-1can be divided into three regions. In the region I and region III, there are both ice formation on the substrate surface. While, the behavior of IWs in the region I and region III are distinguished, including the arrangements of oxygen atoms and the dipole orientation distribution. In region II, ice formation does not occur in the system within 5 × 200 ns simulations. The IWs show a disorder structure, preventing the ice formation process on substrate. The interfacial water molecular orientation distribution and two-dimensional free energy landscape reveals that the electric field can alter the dipole orientation of the interfacial water and lead a free energy barrier, making the ice formation process harder. Our result demonstrates the external electric field can regulate the behavior of IWs, and further affect the ice formation process. The external electric field act as a crystallization switch of ice formation on substrate, shedding light into the studies on the control of ice crystallization.

The role of mechano-regulated YAP/TAZ in erectile dysfunction.

Phosphodiesterase type 5 inhibitors (PDE5is) constitute the primary therapeutic option for treating erectile dysfunction (ED). Nevertheless, a substantial proportion of patients, approximately 30%, do not respond to PDE5i treatment. Therefore, new treatment methods are needed. In this study, we identified a pathway that contributes to male erectile function. We show that mechano-regulated YAP/TAZ signaling in smooth muscle cells (SMCs) upregulates adrenomedullin transcription, which relaxed the SMCs to maintain erection. Using single-nucleus RNA sequencing, we investigated how penile erection stretches the SMCs, inducing YAP/TAZ activity. Subsequently, we demonstrate that YAP/TAZ plays a role in erectile function and penile rehabilitation, using genetic lesions and various animal models. This mechanism relies on direct transcriptional regulation of adrenomedullin by YAP/TAZ, which in turn modulates penile smooth muscle contraction. Importantly, conventional PDE5i, which targets NO-cGMP signaling, does not promote erectile function in YAP/TAZ-deficient ED model mice. In contrast, by activating the YAP/TAZ-adrenomedullin cascade, mechanostimulation improves erectile function in PDE5i nonrespondent ED model rats and mice. Furthermore, using clinical retrospective observational data, we found that mechanostimulation significantly promotes erectile function in patients irrespective of PDE5i use. Our studies lay the groundwork for exploring the mechano-YAP/TAZ-adrenomedullin axis as a potential target in the treatment of ED.

Modular Design for Proteins Assembling into Antifouling Coatings: Case of Gold Surfaces.

We analyze modularity for a B-M-E triblock protein designed to self-assemble into antifouling coatings. Previously, we have shown that the design performs well on silica surfaces when B is taken to be a silica-binding peptide, M is a thermostable trimer domain, and E is the uncharged elastin-like polypeptide (ELP), E = (GSGVP)40. Here, we demonstrate that we can modulate the nature of the substrate on which the coatings form by choosing different solid-binding peptides as binding domain B and that we can modulate antifouling properties by choosing a different hydrophilic block E. Specifically, to arrive at antifouling coatings for gold surfaces, as binding block B we use the gold-binding peptide GBP1 (with the sequence MHGKTQATSGTIQS), while we replace the antifouling blocks E by zwitterionic ELPs of different lengths, EZn = (GDGVP-GKGVP)n/2, with n = 20, 40, or 80. We find that even the B-M-E proteins with the shortest E blocks make coatings on gold surfaces with excellent antifouling against 1% human serum (HS) and reasonable antifouling against 10% HS. This suggests that the B-M-E triblock protein can be easily adapted to form antifouling coatings on any substrate for which solid-binding peptide sequences are available.

A Rational Design of Metal-Organic Framework Nanozyme with High-Performance Copper Active Centers for Alleviating Chemical Corneal Burns.

Metal-organic frameworks (MOFs) have attracted significant research interest in biomimetic catalysis. However, the modulation of the activity of MOFs by precisely tuning the coordination of metal nodes is still a significant challenge. Inspired by metalloenzymes with well-defined coordination structures, a series of MOFs containing halogen-coordinated copper nodes (Cu-X MOFs, X = Cl, Br, I) are employed to elucidate their structure-activity relationship. Intriguingly, experimental and theoretical results strongly support that precisely tuning the coordination of halogen atoms directly regulates the enzyme-like activities of Cu-X MOFs by influencing the spatial configuration and electronic structure of the Cu active center. The optimal Cu-Cl MOF exhibits excellent superoxide dismutase-like activity with a specific activity one order of magnitude higher than the reported Cu-based nanozymes. More importantly, by performing enzyme-mimicking catalysis, the Cu-Cl MOF nanozyme can significantly scavenge reactive oxygen species and alleviate oxidative stress, thus effectively relieving ocular chemical burns. Mechanistically, the antioxidant and antiapoptotic properties of Cu-Cl MOF are achieved by regulating the NRF2 and JNK or P38 MAPK pathways. Our work provides a novel way to refine MOF nanozymes by directly engineering the coordination microenvironment and, more significantly, demonstrating their potential therapeutic effect in ophthalmic disease.

Discovery of Linvencorvir (RG7907), a Hepatitis B Virus Core Protein Allosteric Modulator, for the Treatment of Chronic HBV Infection.

Described herein is the first-time disclosure of Linvencorvir (RG7907), a clinical compound and a hepatitis B virus (HBV) core protein allosteric modulator, for the treatment of chronic HBV infection. Built upon the core structure of hetero aryl dihydropyrimidine, RG7907 was rationally designed by combining all the drug-like features of low CYP3A4 induction, potent anti-HBV activity, high metabolic stability, low hERG liability, and favorable animal pharmacokinetic (PK) profiles. In particular, the chemistry strategy to mitigate CYP3A4 induction through introducing a large, rigid, and polar substituent at the position that has less interaction with the therapeutic biological target (HBV core proteins herein) is of general interest to the medicinal chemistry community. RG7907 demonstrated favorable animal PK, pharmacodynamics, and safety profiles with sufficient safety margins supporting its clinical development in healthy volunteers and HBV-infected patients.

Consistency and Discrepancy between Visibility and PM2.5 Measurements: Potential Application of Visibility Observation to Air Quality Study.

High-quality measurements of air quality are the highest priority for understanding widespread air pollution. Visibility has been widely suggested to be a good alternative to PM2.5 concentration as a measure. In this study, the similarities and differences between visibility and PM2.5 measurements in China are checked and the results reveal the potential application of visibility observation to the study of air quality. Based on the quality-controlled PM2.5 and visibility data from 2016 to 2018, the nonparametric Spearman correlation coefficient (ρ) values between stations for PM2.5 and visibility-derived surface extinction coefficient (bext) decrease as the station distance (R) increases. Some relatively low ρ values (<0.4) occur in regions characterized by the lowest (background) levels of PM2.5 and bext values, for example, the Tibetan and Yungui Plateau. The relatively lower ρ for bext compared to PM2.5 is probably caused by the predefined maximum threshold of visibility measurements (generally 30 km). A significant correlation between PM2.5 and bext is derived in most stations and relatively larger ρ values are evident in eastern China (Northeast China excluded) and in winter (the national median ρ is 0.67). The abrupt changes in specific mass extinction efficiency (αext) imply a potentially large influence of alternation of visibility sensors or recalibrations on visibility measurements. The bext data are thereafter corrected by comparison to the reference measurements at the adjacent stations, which leads to a three-year quality assured of visibility and bext datasets.

Oriented Crystallization of Hydroxyapatite in Self-Assembled Peptide Fibrils as a Bonelike Material.

Controlling oriented crystallization is key to producing bonelike composite materials with a well-organized structure. However, producing this type of composite material using synthetic biopolymers as scaffolds is challenging. Inspired by the molecular structure of collagen-I, a collagenlike peptide─(Pro-Hyp-Gly)10 (POG10)─was designed to produce self-assembled fibrils that resemble the structure of collagen-I fibrils. In addition, the oriented mineralization of HAP crystals is formed in the fibrils that reproduces a bonelike material similar to collagen-I fibril mineralization. Unlike collagen-I fibrils, POG10 fibrils do not contain gap spaces. The molecular simulation results indicate that in addition to space confinement, the molecular field generated by POG10 can also confine the orientation of HAP, enriching our understanding of physical confinement and shedding light on the design of synthetic biopolymer scaffolds for bonelike material fabrication.