Computational analysis of PD-L1 dimerization mechanism induced by small molecules and potential dynamical properties.

The design of small molecule inhibitors that target the programmed death ligand-1 (PD-L1) is a forefront issue in immune checkpoint blocking therapy. Small-molecule inhibitors have been shown to exert therapeutic effects by inducing dimerization of the PD-L1 protein, however, the specific mechanisms underlying this dimerization process remain largely unexplored. Furthermore, there is a notable lack of comparative studies examining the binding modes of structurally diverse inhibitors. In view of the research gaps, this work employed molecular dynamics simulations to meticulously examine the interactions between two distinct types of inhibitors and PD-L1 in both monomeric and dimeric forms, and predicted the dimerization mechanism. The results revealed that inhibitors initially bind to a PD-L1 monomer, subsequently attracting another monomer to form a dimer. Notably, symmetric inhibitors observed superior binding efficiency compared to other inhibitors. Key residues, including Ile54, Tyr56, Met115 and Tyr123 played a leading role in binding. Structurally, symmetric inhibitors were capable of thoroughly engaging the binding pocket, promoting a more symmetrical formation of PD-L1 dimers. Furthermore, symmetric inhibitors formed more extensive hydrophobic interactions with protein residues. The insights garnered from this research are expected to significantly contribute to the rational design and optimization of small molecule inhibitors targeting PD-L1.

Exploring the potential of VGLL3 methylation as a prognostic indicator for intracranial aneurysm with gender-specific considerations.

DNA methylation is widely recognized to play a role in intracranial aneurysm (IA) pathogenesis. We investigated the levels of methylation of vestigial-like 3 (VGLL3) in IA and explored its potential as a prognostic indicator. A total of 48 patients with IA and 48 healthy controls were included in the present study. Methylation levels of CpG sites were assessed using bisulfite pyrosequencing, and levels of VGLL3, TEAD, and YAP in the blood were measured by real-time quantitative polymerase chain reaction testing. VGLL3 methylation was significantly higher in controls than in IA patients (P=0.001), and this phenomenon was more pronounced in females (P<0.001). Compared with the control group, the expression levels of VGLL3 and TEAD in the blood of IA patients were significantly increased, while YAP was significantly decreased. VGLL3 methylation was positively correlated with HDL (P=0.003) and female Lpa concentration (r = 0.426, P=0.03), and was also negatively correlated with age (P=0.003), APOE (P=0.005), and VGLL3 mRNA expression (P<0.001). Methylation and mRNA expression of VGLL3 may serve as indicators of IA risk in females (AUC = 0.810 and 0.809). VGLL3 methylation may participate in the pathogenesis of IA by regulating the expression of the VGLL3/TEAD/YAP pathway, and its gene methylation and expression levels have IA risk prediction value.

The impact of osteoporosis and diabetes on fracture healing under different loading conditions.

BACKGROUND: Osteoporosis and diabetes are two prevalent conditions among the elderly population. Each of these conditions can profoundly influence the fracture healing process by disturbing the associated inflammatory process. However, the combined effects of osteoporosis and diabetes on fracture healing remain unclear. Therefore, the purpose of the present study is to investigate the role of osteoporosis and diabetes in fracture healing and the underlying mechanisms by developing numerical models. METHOD: This study introduces a numerical model that consists of a three-dimensional model of a tibia fracture stabilized by a Locking Compression Plate (LCP), coupled with a two-dimensional axisymmetric model which illustrates the transport and reactions of cells and cytokines throughout the inflammatory phase in early fracture healing. First, the model parameters were calibrated using available experimental data. The model was then implemented to predict the healing outcomes of fractures under five varied conditions, consisting of both osteoporotic and non-osteoporotic bones, each subjected to different physiological loads. RESULTS: The instability of the fracture callus can significantly escalate in osteoporotic fractures (e.g., when a 150 N physiological load is applied, the unstable region of the osteoporotic fracture callus can reach 26 %, in contrast to 12 % in non-osteoporotic fractures). Additionally, the mesenchymal stem cells (MSCs) proliferation and differentiation can be disrupted in osteoporotic fracture compared to non-osteoporotic fractures (e.g., on the 10th day post-fracture, the decrease in the concentration of MSCs, osteoblasts, and chondrocytes in osteoporotic fractures is nearly double that in non-osteoporotic fractures under a 150 N). Finally, the healing process of fractures can suffer significant impairment when osteoporosis coexists with diabetes (e.g., the concentration of MSCs can be drastically reduced by nearly 37 % in osteoporotic fractures under diabetic conditions when subjected to a load of 200 N) CONCLUSIONS: Fracture calluses destabilized by osteoporosis can negatively affect the fracture healing process by disrupting the proliferation and differentiation of mesenchymal stem cells (MSCs). Moreover, when osteoporosis coexists with diabetes, the fracture healing process can severely impair the fracture healing outcomes.

d-Glucosamine induces circadian phase delay by promoting BMAL1 degradation through AMPK/mTOR pathway.

Circadian rhythms are closely linked to the metabolic network through circadian feedback regulation. The hexosamine biosynthetic pathway (HBP) is a branch of glucose metabolism that affects circadian rhythms through the O-linked N-acetylglucosamine modification (O-GlcNAcylation) of clock proteins. Here, we found out that, among the downstream metabolites regulated by d-glucosamine (GlcN) in HBP salvage pathway, only GlcN is able to induce circadian phase delay both in vitro and in vivo. Mechanistic studies indicated that the phase-shift induced by GlcN is independent of O-GlcNAcylation. Instead, GlcN selectively up-regulates p-AMPK activity, leading to the inhibition of mTOR signaling pathway, and thus down-regulation of p-BMAL1 both in human cell line and mouse tissues. Moreover, GlcN promoted BMAL1 degradation via proteasome pathway. These findings reveal a novel molecular mechanism of GlcN in regulating clock phase and suggest the therapeutic potential of GlcN as new use for an old drug in the future treatment of shift work and circadian misalignment.

The effects of mechanical instability on PDGF mediated inflammatory response at early stage of fracture healing under diabetic condition.

BACKGROUND AND OBJECTIVE: Mechanical stability plays an important role in fracture healing process. Excessive interfragmentary movement will continuously damage the tissue and newly formed capillaries at the fracture site, which leads to overproduction of platelet-derived growth factor (PDGF) that attracts more macrophages into fracture callus, ultimately persistent and enhanced inflammatory response happens. For diabetic condition, the impact of mechanical instability of fracture site on inflammatory response could be further compliciated and the relevant research in this field is relatively limited. METHODS: Building on previous experimental studies, this study presents a numerical model consisting of a system of reactive-transport equations representing the transport as well as interactions of different cells and cytokines within the fracture callus. The model is initially validated by available experimental data, and then implemented to investigate the role of mechanical stability of fracture site in inflammatory response during early stage of healing. It is assumed that there is an increased release of PDGF due to the rupture of blood vessels resulting from mechanical instability, which leads to increased production of inflammatory cytokines (i.e., TNF-α). The bone healing process under three different conditions were investigated, i.e., mechanically stable condition with normal inflammatory response (Control, Case 1), mechanically unstable condition with normal inflammatory response (Case 2) and mechanically unstable condition with diabetes (Case 3). RESULTS: Mechanical instability can promote the macrophage infiltration and thus induce an enhanced and prolonged inflammatory response, which could impede the MSCs proliferation during the early fracture healing stage (e.g., compared with the control condition, the MSCs concentration in unstable fracture with normal inflammatory response can be reduced by 3.2% and 5.2% on day 2 and day 10 post-fracture, respectively). Under diabetic condition, the mechanical instability of fracture site could lead to a significant increase of TNF-α concentration in fracture callus (Case 3) in comparison to control (Case 1) (e.g., three-fold increase in TNF-α concentration compared to control). In addition, the results show that the mechanical instability affects the cell differentiation and proliferation in fracture callus in a spatially dependent manner, e.g., for diabetic fracture patients, the mechanical instability could potentially decrease the concentration of MSCs, osteoblasts and chondrocytes by around 39%, 30% and 29% in cortical callus, respectively, in comparison to control. CONCLUSION: The mechanical instability together with diabetic condition can significantly affect the natural resolution of inflammation during early stage of healing by turning acute inflammation into chronic inflammation which is characterized by a continuously upregulated TNF-α pathway.

Role of TNF-α in early-stage fracture healing under normal and diabetic conditions.

BACKGROUND AND OBJECTIVE: Inflammatory response plays a crucial role in the early stage of fracture healing. Immediately after fracture, the debris and immune cells (e.g., macrophages), recruited into the fracture callus, lead to the secretion of inflammatory cytokines, such as tumor necrosis factor-alpha (TNF-α), which governs the mesenchymal stem cells (MSCs) mediated healing processes. However, it is still unclear how chronic inflammatory diseases (e.g., diabetes) affect the level of TNF-α in fracture callus, ultimately the healing outcomes at the early stage of healing. Therefore, the purpose of this study is to develop a numerical model for investigating TNF-α mediated bone fracture healing. METHODS: A mathematical model consisting of a system of partial differential equations that represent the reactive transport of cells and cytokines in the fracture callus is developed in this study. The model is first calibrated by using available experimental data and then implemented to study the effect of TNF-α on the early stage of fracture healing under normal and diabetic conditions. RESULTS: There is a significant elevation of TNF-α level in facture callus during the first 24 h post-fracture in normal condition, and its influence in the concentration of MSCs and cell differentiation becomes significant three days post-fracture (e.g., the absence of TNF-α signaling could reduce the concentration of MSCs more than 20% in cortical callus). In addition, the excessive secretion of TNF-α induced by diabetes could decrease the concentration of MSCs at the initial stage of healing, particularly reduce the concentration of MSCs in cortical callus by around 25%. CONCLUSION: The model predictions suggested that there should be an optimal concentration of TNF-α in fracture callus, which enhances the early stage of healing, and excessive or insufficient secretion of TNF-α might significantly hinder the healing process.

Reaction mechanism of chloramphenicol with hydroxyl radicals for advanced oxidation processes using DFT calculations.

The structure properties of chloramphenicol (CAP), including bond information and the Fukui function for the atoms in the main chain, were investigated computationally by density functional theory (DFT). The result shows that the chiral carbons in CAP offer the most active positions for chemical reactions, which is in good agreement with the experiment. The detailed degradation mechanism for CAP with hydroxyl radicals in advanced oxidation processes is further studied at the SMD/M06-2X/6-311 + G(d,p) level of theory. The main reaction methods, including the addition-elimination reaction, hydrogen abstract reaction, hydroxyl radical addition, and bond-breaking processes, are calculated. The results show that the nitro-elimination reaction is the most likely reaction in the first step of the degradation of CAP, and the latter two processes are more likely to be hydrogen abstract reactions. The details for the transition states, intermediate radicals, and free energy surfaces for all proposed reactions are given, which makes up for a lack of experimental knowledge.

Efficacy and safety of rivaroxaban on the resolution of left atrial/left atrial appendage thrombus in nonvalvular atrial fibrillation patients.

Data on LA/LAA thrombus resolution after rivaroxaban treatment has not been established. The aim of the present study was to compare the efficacy and safety on the resolution of LA/LAA thrombus between rivaroxaban and warfarin in nonvalvular atrial fibrillation (AF) patients. 80 AF patients with LA/LAA thrombus between January 2013 and June 2016 were randomized divided into warfarin group (n = 40) and rivaroxaban group (n = 40). Compared to warfarin group, thrombin time (TT; p < 0.0001), plasma prothrombin time (PT; p < 0.0001), and activated partial thromboplastin time (APTT; p = 0.0019) were significantly lower, and fibrinogen (FIB; p < 0.0001) was significantly higher in rivaroxaban group. TEE shown the average length (p < 0.0001), average width (p = 0.0008) and average area (p < 0.0001) of thrombus were significantly lower in rivaroxaban group compared to warfarin group after 6-week treatments. No major or fatal bleeding and ischemic stroke occurred in both two groups. The 20 mg dose Rivaroxaban is more effective than warfarin on the resolution of LA/LAA thrombus in nonvalvular AF patients especially after 6-week treatments. The results suggest that rivaroxaban is a potential option for the treatment of LA/LAA thrombus in patients with nonvalvular AF.

Bifunctional oxygen electrocatalyst derived from photochlorinated graphene for rechargeable solid-state Zn-air battery.

Photochlorination method was used to engineer the structural defects and covalent CCl bonds in graphene. Cl coverage of 18 atom% was successfully confirmed by X-ray photoelectron spectroscopy, and D, G and 2D peaks changes upon irradiation were monitored by Raman. The mobility of chlorinated graphene field-effect transistor decreased to 66.1 cm2/(V s) in comparison to pristine graphene of 730.4 cm2/(V s). Raman indicated that the defects and CCl bonds are sensitively associated with the irradiation time, thus the structural defects and composition can be engineered accordingly. Given the creation of active sites, namely the polarization of carbon, as well as fast ionic and electronic transport, chlorinated graphene has demanded features for electrocatalytic reactions. As a proof of concept, chlorinated vertically-oriented graphene grown on carbon cloth (CC@VG) served as excellent bifunctional oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) free-standing electrodes, showing overpotential of 405 mV for OER, Tafel slope of 56 mV, which has better durability than that of commercial Ir/C. Meanwhile, the ORR reduction peak appeared at 0.776 V vs. RHE, more positive than that of carbon cloth (0.60 V). All-solid-state Zn-air battery (ZABs) using chlorinated CC@VG as bifunctional air-cathode showed stable discharge voltage of 1.28 V at current density of 2 mA/cm2, power density of 45.8 mW/cm2 at 80 mA/cm2. More than 108 discharge/charge cycles (20 min per cycle) was obtained at current density of 2 mA/cm2, and round-trip efficiency decreased from 57.4% to 50.0%. Present work developed a universal chlorination method to endow carbonaceous materials with abundant defects and polarized carbon as active site as efficient bifunctional electrocatalysts, and opened a new avenue for developing promising air-cathodes for rechargeable solid-state ZABs.

Budesonide, but not dexamethasone, blunted the response of aldosterone to renin elevation by suppressing angiotensin converting enzyme upon high-altitude exposure.

INTRODUCTION: Inhaled budesonide is a novel approach to prevent acute mountain sickness (AMS). However, its mechanism is not completely understood. We aimed to investigate the effects of budesonide and dexamethasone on renin-angiotensin-aldosterone system in AMS prevention. MATERIALS AND METHODS: Data were obtained from a randomised controlled trial including 138 participants. The participants were randomly assigned to receive budesonide, dexamethasone or placebo as prophylaxis before they travelled to 3450 m altitude from 400 m by car. Their plasma concentrations of renin, angiotensin-converting enzyme (ACE) and aldosterone were measured at both altitudes. RESULTS: All parameters were comparable among the three groups at 400 m. After high-altitude exposure of 3450, renin in all groups increased significantly; the ACE, aldosterone concentrations, as well as the aldosterone/renin ratio, rose markedly in the dexamethasone and placebo groups but not in the budesonide group. Moreover, the aldosterone/renin ratio correlated closely with ACE concentration. CONCLUSIONS: Upon acute high-altitude exposure, budesonide, but not dexamethasone, blunted the response of aldosterone to renin elevation by suppressing angiotensin converting enzyme.

Variants of the low oxygen sensors EGLN1 and HIF-1AN associated with acute mountain sickness.

Two low oxygen sensors, Egl nine homolog 1 (EGLN1) and hypoxia-inducible factor 1-α inhibitor (HIF-1AN), play pivotal roles in the regulation of HIF-1α, and high altitude adaption may be involved in the pathology of acute mountain sickness (AMS). Here, we aimed to analyze single nucleotide polymorphisms (SNPs) in the untranslated regions of the EGLN1 and HIF-1AN genes and SNPs chosen from a genome-wide adaptation study of the Han Chinese population. To assess the association between EGLN1 and HIF-1AN SNPs and AMS in a Han Chinese population, a case-control study was performed including 190 patients and 190 controls. In total, thirteen SNPs were genotyped using the MassARRAY® MALDI-TOF system. Multiple genetic models were tested; The Akaike's information criterion (AIC) and Bayesian information criterion (BIC) values indicated that the dominant model may serve as the best-fit model for rs12406290 and rs2153364 of significant difference. However, these data were not significant after Bonferroni correction. No significant association was noted between AMS and rs12757362, rs1339894, rs1361384, rs2009873, rs2739513 or rs2486729 before and after Bonferroni correction. Further haplotype analyses indicated the presence of two blocks in EGLN1; one block consists of rs12406290-rs2153364, located upstream of the EGLN1 gene. Carriers of the "GG" haplotype of rs12406290-rs2153364 exhibited an increased risk of AMS after adjustments for age and smoking status. However, no significant association was observed among HIF-1AN 3'-untranslated region (3'-UTR) polymorphisms, haplotype and AMS. Our study indicates that variants in the EGLN1 5'-UTR influence the susceptibility to AMS in a Han Chinese population.