Hydrophobic substrate binding pocket remodeling of echinocandin B deacylase based on multi-dimensional rational design.

Actinoplanes utahensis deacylase (AAC)-catalyzed deacylation of echinocandin B (ECB) is a promising method for the synthesis of anidulafungin, the newest of the echinocandin antifungal agents. However, the low activity of AAC significantly limits its practical application. In this work, we have devised a multi-dimensional rational design strategy for AAC, conducting separate analyses on the substrate-binding pocket's volume, curvature, and length. Furthermore, we quantitatively analyzed substrate properties, particularly on hydrophilic and hydrophobic. Accordingly, we tailored the linoleic acid-binding pocket of AAC to accommodate the extended long lipid chain of ECB. By fine-tuning the key residues, the resulting AAC mutants can accommodate the ECB lipid chain with a lower curvature binding pocket. The D53A/I55F/G57M/F154L/Q661L mutant (MT) displayed 331 % higher catalytic efficiency than the wild-type (WT) enzyme. The MT product conversion was 94.6 %, reaching the highest reported level. Utilizing a multi-dimensional rational design for a customized mutation strategy of the substrate-binding pocket is an effective approach to enhance the catalytic efficiency of enzymes in handling complicated substrates.

Is short-term exposure to primary gaseous air pollutants associated with AIDS-related deaths? Evidence from a time-stratified case-crossover study.

Primary gaseous air pollutants have been associated with death from multiple causes, however, it remains unknown if they play a role in premature mortality among individuals living with HIV/AIDS. Data on HIV/AIDS patients were collected from the Hubei Provincial Center for Disease Control and Prevention, with a total of 1,467 AIDS-related deaths (ARD) between 2013 and 2020. Daily mean sulfur dioxide (SO2), nitrogen dioxide (NO2), and carbon monoxide (CO) were generated by artificial intelligence algorithms combined with big data. We employed a time-stratified case-crossover approach and conditional logistical regression models to investigate the acute effects of primary gaseous air pollutants on ARD. Per interquartile range increase in the concentrations of SO2 was significantly linked with ARD, with a corresponding odds ratio (OR) of 1.17 [95% confidence intervals (CIs): 1.01, 1.35] at lag 4 day. Furthermore, our findings indicated that males exhibited a heightened vulnerability to the adverse effects of SO2 and NO2, for example, the ORs were 1.24 (95% CIs: 1.05, 1.47) and 1.16 (95% CIs: 1.01, 1.34), respectively. Moreover, individuals aged over 65 years were more susceptible to SO2 and CO. Additionally, we identified the warm season as a sensitive period for mortality associated with SO2 and NO2. Our study furnished fresh evidence regarding the detrimental effects of primary gaseous air pollutants on ARD.

Food therapy of scutellarein ameliorates pirarubicin­induced cardiotoxicity in rats by inhibiting apoptosis and ferroptosis through regulation of NOX2­induced oxidative stress.

Pirarubicin (THP) is one of the most commonly used antineoplastic drugs in clinical practice. However, its clinical application is limited due to its toxic and heart­related side effects. It has been reported that oxidative stress, inflammation and apoptosis are closely associated with cardiotoxicity caused by pirarubicin (CTP). Additionally, it has also been reported that scutellarein (Sc) exerts anti­inflammatory, antioxidant, cardio­cerebral vascular protective and anti­apoptotic properties. Therefore, the present study aimed to investigate the effect of food therapy with Sc on CTP and its underlying molecular mechanism using echocardiography, immunofluorescence, western blot, ROS staining, and TUNEL staining. The in vivo results demonstrated that THP was associated with cardiotoxicity. Additionally, abnormal changes in the expression of indicators associated with oxidative stress, ferroptosis and apoptosis were observed, which were restored by Sc. Therefore, it was hypothesized that CTP could be associated with oxidative stress, ferroptosis and apoptosis. Furthermore, the in vitro experiments showed that Sc and the NADPH oxidase 2 (NOX2) inhibitor, GSK2795039 (GSK), upregulated glutathione peroxidase 4 (GPX4) and inhibited THP­induced oxidative stress, apoptosis and ferroptosis. However, cell treatment with the ferroptosis inhibitor, ferrostatin­1, or inducer, erastin, could not significantly reduce or promote, respectively, the expression of NOX2. However, GSK significantly affected ferroptosis and GPX4 expression. Overall, the results of the present study indicated that food therapy with Sc ameliorated CTP via inhibition of apoptosis and ferroptosis through regulation of NOX2­induced oxidative stress, thus suggesting that Sc may be a potential therapeutic drug against CTP.

Method for the extraction of circulating nucleic acids based on MOF reveals cell-free RNA signatures in liver cancer.

Cell-free RNA (cfRNA) allows assessment of health, status, and phenotype of a variety of human organs and is a potential biomarker to non-invasively diagnose numerous diseases. Nevertheless, there is a lack of highly efficient and bias-free cfRNA isolation technologies due to the low abundance and instability of cfRNA. Here, we developed a reproducible and high-efficiency isolation technology for different types of cell-free nucleic acids (containing cfRNA and viral RNA) in serum/plasma based on the inclusion of nucleic acids by metal-organic framework (MOF) materials, which greatly improved the isolation efficiency and was able to preserve RNA integrity compared with the most widely used research kit method. Importantly, the quality of cfRNA extracted by the MOF method is about 10-fold that of the kit method, and the MOF method isolates more than three times as many different RNA types as the kit method. The whole transcriptome mapping characteristics of cfRNA in serum from patients with liver cancer was described and a cfRNA signature with six cfRNAs was identified to diagnose liver cancer with high diagnostic efficiency (area under curve = 0.905 in the independent validation cohort) using this MOF method. Thus, this new MOF isolation technique will advance the field of liquid biopsy, with the potential to diagnose liver cancer.

Effect of stearoyl-coenzyme a desaturase 1 (SCD1) on the function of mast cells.

Background: The prevalence of childhood asthma and obesity is increasing, while obesity increases the risk and severity of asthma. Lipid metabolism has been considered as an important factor in the pathogenesis of obesity-associated asthma. Stearoyl-CoA desaturase 1 (SCD1) is a rate-limiting enzyme that catalyzes the production of monounsaturated fatty acids (MUFA).Methods: In the present study, the microarray data retrieved from the Gene Expression Comprehensive Database (GEO) was analyzed to further clarify the impact of SCD1 on Mast cell activation related lipid mediators and the correlation between SCD1 and obesity asthma in the population.Results: SCD1 was highly expressed in IgE-activated bone marrow-derived mast cells (BMMCs). Meanwhile, SCD1 was also verified expressed highly in dinitrophenyl human serum albumin (DNP-HAS) stimulated RBL-2H3 cells. The expression of SCD1 was up-regulated in peripheral blood leukocytes of asthmatic children, and was positively correlated with skinfold thickness of upper arm, abdominal skinfold and body mass index (BMI). Inhibition of SCD1 expression significantly suppressed the degranulation, lipid mediator production, as well as the migration ability in DNP-HAS-stimulated RBL-2H3 cells.Conclusion: SCD1 is involved in obese-related asthma through regulating mast cells.

The role of TRPV4 in programmed cell deaths.

Programmed cell death is a major life activity of both normal development and disease. Necroptosis is early recognized as a caspase-independent form of programmed cell death followed obviously inflammation. Apoptosis is a gradually recognized mode of cell death that is characterized by a special morphological changes and unique caspase-dependent biological process. Ferroptosis, pyroptosis and autophagy are recently identified non-apoptotic regulated cell death that each has its own characteristics. The transient receptor potential vanilloid 4 (TRPV4) is a kind of nonselective calcium-permeable cation channel, which is received more and more attention in biology studies. It is widely expressed in human tissues and mainly located on the membrane of cells. Several researchers have identified that the influx Ca2+ from TRPV4 acts as a key role in the loss of cells by apoptosis, ferroptosis, necroptosis, pyroptosis and autophagy via mediating endoplasmic reticulum (ER) stress, oxidative stress and inflammation. This effect is bad for the normal function of organs on the one hand, on the other hand, it is benefit for anticancer activities. In this review, we will summarize the current discovery on the role and impact of TRPV4 in these programmed cell death pathological mechanisms to provide a new prospect of gene therapeutic target of related diseases.

Transcriptome analysis of axillary buds in low phosphorus stress and functional analysis of TaWRKY74s in wheat.

BACKGROUND: Wheat is one of the main grain crops in the world, and the tiller number is a key factor affecting the yield of wheat. Phosphorus is an essential element for tiller development in wheat. However, due to decreasing phosphorus content in soil, there has been increasing use of phosphorus fertilizer, while imposing risk of soil and water pollution. Hence, it is important to identify low phosphorus tolerance genes and utilize them for stress resistance breeding in wheat. RESULTS: We subjected the wheat variety Kenong 199 (KN199) to low phosphorus stress and observed a reduced tiller number. Using transcriptome analysis, we identified 1651 upregulated genes and 827 downregulated of genes after low phosphorus stress. The differentially expressed genes were found to be enriched in the enzyme activity regulation related to phosphorus, hormone signal transduction, and ion transmembrane transport. Furthermore, the transcription factor analysis revealed that TaWRKY74s were important for low phosphorus tolerance. TaWRKY74s have three alleles: TaWRKY74-A, TaWRKY74-B, and TaWRKY74-D, and they all belong to the WRKY family with conserved WRKYGQK motifs. These proteins were found to be located in the nucleus, and they were expressed in axillary meristem, shoot apical meristem(SAM), young leaves, leaf primordium, and spikelet primordium. The evolutionary tree showed that TaWRKY74s were closely related to OsWRKY74s in rice. Moreover, TaWRKY74s-RNAi transgenic plants displayed significantly fewer tillers compared to wild-type plants under normal conditions. Additionally, the tiller numebr of the RNAi transgenic plants was also significantly lower than that of the wild-type plants under low-phosphorus stress, and increased the decrease amplitude. This suggestd that TaWRKY74s are related to phosphorus response and can affect the tiller number of wheat. CONCLUSIONS: The results of this research showed that TaWRKY74s were key genes in wheat response to low phosphorus stress, which might regulate wheat tiller number through abscisic acid (ABA) and auxin signal transduction pathways. This research lays the foundation for further investigating the mechanism of TaWRKY74s in the low phosphorus environments and is significant for wheat stress resistance breeding.

Integrative study of pulmonary microbiome, transcriptome and clinical outcomes in Mycoplasma pneumoniae pneumonia.

BACKGROUND: This study aimed to investigate the interactions among three core elements of respiratory infection-pathogen, lung microbiome, and host response-and their avocation with the severity and outcomes of Mycoplasma pneumoniae pneumonia (MPP) in children. METHODS: We prospectively collected bronchoalveolar lavage fluid from a cohort of 41 children with MPP, including general MPP (GMPP) and complicated MPP (CMPP), followed by microbiome and transcriptomic analyses to characterize the association among pathogen, lung microbiome, and host response and correlate it with the clinical features and outcomes. RESULTS: The lung microbiome of patients with CMPP had an increased relative abundance of Mycoplasma pneumoniae (MP) and reduced alpha diversity, with 76 differentially expressed species. Host gene analysis revealed a key module associated with neutrophil function and several inflammatory response pathways. Patients with a high relative abundance of MP, manifested by a specific lung microbiome and host response type, were more prone to CMPP and had a long imaging recovery time. CONCLUSION: Patients with CMPP have a more disrupted lung microbiome than those with GMPP. MP, lung microbiome, and host response interacts with each other and are closely related to disease severity and outcomes in children with MPP.

Bioinformatics and experimental studies jointly reveal that Sacubitril Valsartan improves myocardial oxidative stress and inflammation by regulating the MAPK signaling pathway to treat chemotherapy related cardiotoxicity.

BACKGROUND: CRC is a common but serious complication or sequela of tumor treatment, and new coping strategies are urgently needed. SV is a classic clinical cardiovascular protective drug, which has been widely used in the treatment of heart failure, hypertension and other diseases. It has good therapeutic effect in other cardiovascular diseases such as diabetes cardiomyopathy, ischemic cardiomyopathy and vascular disease, but it has not been proved by research that SV can prevent and treat CRC. METHOD: In this study, DOX was used to induce a rat CRC model and evaluate the therapeutic effect of SV on it. Subsequently, R software was applied to analyze the control group, SV group, and DOX group in databases GSE207283 and GSE22369, and to screen for common differentially expressed genes. Use the DAVID website for enrichment analysis and visualization. Use STRING website to analyze and visualize protein interaction networks of key genes. Finally, experimental verification was conducted on key genes. RESULT: Our research results show that SV has a protective effect on DOX induced myocardial injury by alleviating Weight loss, increasing Ejection fraction, and reducing the level of biomarkers of myocardial injury. Meanwhile, SV can effectively alleviate the above abnormalities. Bioinformatics and KEGG pathway analysis showed significant enrichment of metabolic and MAPK signaling pathways, suggesting that they may be the main regulatory pathway for SV treatment of CRC. Subsequent studies have also confirmed that SV can inhibit DOX induced myocardial injury through the MAPK signaling pathway, and alleviate DOX induced oxidative stress and inflammatory states. CONCLUSION: Our research indicates that SV is a potential drug for treating CRC and preliminarily elucidates its molecular mechanism of regulating the MAPK pathway to improve oxidative stress and inflammation.

Ambient temperature variations and AIDS-related mortality: A time-stratified case-crossover study in 103 counties, China.

BACKGROUND: Climate change, characterized by the steady ascent of global temperatures and the escalating unpredictability of climate patterns, poses multifaceted challenges to public health worldwide. However, vulnerable groups, particularly the population affected by HIV/AIDS, have received little attention. OBJECTIVES: We aimed to examine the impacts of temperature variations on AIDS-related mortality. METHODS: Data on individuals with HIV/AIDS were collected from the HIV/AIDS Comprehensive Response Information Management System between 2013 and 2019. Temperature variation metrics were constructed by diurnal temperature range (DTR), temperature changes between neighboring days (TCN), and temperature variability (TV0-t). Time-stratified case-crossover design with conditional logistic regression models was used to investigate the associations between ambient temperature variations and AIDS-related mortality. RESULTS: Each 1 °C elevated in DTR was linked with a 5.28 % [95 % confidence intervals (CIs): 1.61, 9.08] increment in AIDS-related mortality at a lag of 0-6 days. Stronger associations between DTR and AIDS-related mortality were observed in the married than in single, with corresponding excess ORs (%) of 5.33 (95 % CIs: 0.29, 10.62) versus 4.79 (95 % CIs: -0.50, 10.36) for 1 °C increased in DTR at lag 0-6 days. Additionally, we noticed the impact of DTR was more pronounced in the warm season, leading to a 7.32 % (95 % CIs: 0.57, 14.51) elevation in the risks of AIDS-related mortality for 1 °C increase in DTR at lag 0-6 days, while the effect value decreased to 5.16 % (95 % CIs: 0.71, 9.81) in the cold season. CONCLUSIONS: Our findings indicated that DTR might be a significant risk factor for AIDS-related deaths among ambient temperature variation indicators, and underscored the importance of considering temperature variability in public health interventions aimed at mitigating this risk of AIDS-related mortality.

Rational design peptide inhibitors of Cyclophilin D as a potential treatment for acute pancreatitis.

Cyclophilin D (CypD) is a mitochondrial matrix peptidyl prolidase that regulates the mitochondrial permeability transition pore. Inhibition of CypD was suggested as a therapeutic strategy for acute pancreatitis. Peptide inhibitors emerged as novel binding ligand for blocking receptor activity. In this study, we present our computational approach for designing peptide inhibitors of CypD. The 3-D structure of random peptides were built, and docked into the active center of CypD using Rosetta script integrated FlexPepDock module. The peptide displayed the lowest binding energy against CypD was further selected for virtual iterative mutation based on virtual mutagenesis and molecular docking. Finally, the top 5 peptides with the lowest binding energy was selected for validating their affinity against CypD using inhibitory assay. We showed 4 out of the selected 5 peptides were capable for blocking the activity of CypD, while WACLQ display the strongest affinity against CypD, which reached 0.28 mM. The binding mechanism between WACLQ and CypD was characterized using molecular dynamics simulation. Here, we proved our approach can be a robust method for screening peptide inhibitors.

Correlation Analysis of Key Residue Sites between Computational-Aided Design Thermostability d-Amino Acid Oxidase and Ancestral Enzymes.

The d-amino acid oxidase (DAAO) from Rhodotorula taiwanensis has proven to have great potential for applications due to its excellent catalytic kinetic parameters. However, its poor thermal stability has limited its performance in biocatalysis. Herein, starting from the variant SHVG of RtwDAAO, this study employed a comprehensive computational design approach for protein stability engineering, resulting in positive substitutions at specific sites (A43S, T45M, C234L, E195Y). The generated variant combination, SHVG/SMLY, exhibited a significant synergistic effect, leading to an extension of the half-life and Tmapp. The ancestral sequence reconstruction revealed the conservation of the variant sites. The association of the variant sites with the highly stable ancestral enzyme was further explored. After determining the contribution of the variant sites to thermal stability, it was applied to other homologous sequences and validated. Molecular dynamics simulations indicated that the increased hydrophobicity of the variant SHVG/SMLY was a key factor for the increased stability, with strengthened intersubunit interactions playing an important role. In addition, the physical properties of the amino acids themselves were identified as crucial factors for thermal stability generality in homologous enzymes, which is important for the rapid acquisition of a series of stable enzymes.

Assessing multiple factors affecting the gut microbiome structure of very preterm infants.

The composition and diversity of the gut microbiota are essential for the health and development of the immune system of infants. However, there is limited information on factors that influence the gut microbiota of very preterm infants. In this study, we analyzed factors that affect the gut microbiota of very preterm infants. The stool samples from 64 very preterm infants with a gestational age less than 32 weeks were collected for 16S rRNA gene sequencing. The infants were divided according to the delivery mode, antibiotic use during pregnancy, and feeding methods. The abundance of Proteobacteria was high in both cesarean (92.7%) and spontaneous (55.5%) delivery groups and then shifted to Firmicutes after the first week of birth. In addition, Proteobacteria was also the dominant phylum of infant gut microbiome for mothers with antibiotic use, with more than 50% after the first week of birth. In comparison, the dominant phylum for mothers without antibiotic use was Firmicutes. Proteobacteria level was also high in breastfeeding and mixed-feeding groups, consisting of more than 90% of the community. By contrast, Proteobacteria was the dominant phylum at the first week of birth but then shifted to Firmicutes for the formula-fed group. The alterations of gut microbiota in infants can affect their health condition during growth. This study confirmed that the different feeding types, delivery modes, and use of antibiotics during pregnancy can significantly affect the composition of the gut microbiota of very preterm infants.

Submicronic particulate matter (PM1), a "neglected killer" for HIV/AIDS patients in Hubei, China: Results from a cohort study from 2001 to 2020.

BACKGROUND: Although with the progress of antiretroviral therapy, the life expectancy of HIV/AIDS patients was still not equal to that of normal people. Submicronic particulate matter (PM1) might play a role in mortality among people living with HIV/AIDS, However, cohort evidence is extensively scarce. METHODS: This twenty-year open cohort study involved all individuals officially diagnosed with HIV/AIDS in Hubei Province from 2001 to 2020. Time-varying Cox proportional hazard models were applied to investigate the associations between long-term exposure to PM1 and mortality in HIV/AIDS patients. The concentration-response curves between PM1 and AIDS-related deaths/all-cause deaths were characterized by fitting restricted cubic spline models. These curves were then utilized to estimate the number of deaths attributed to PM1. RESULTS: Long-term exposure to PM1 was significantly associated with AIDS-related deaths and all-cause death among HIV/AIDS patients, with excess risks of 2.33 % [95 % confidence interval (CIs): 1.62, 3.15] and 0.69 % (0.22, 1.17) for each 1 µg/m3 increase in annual PM1. HIV-positive people with lower initial CD4+ cell count levels or aged over 65 years old were more susceptible to PM1 exposure. We estimated about 844 AIDS-related deaths and 1175 all-cause deaths can be attributable to ambient PM1 exposure, accounting for 41.7 % and 23.8 % of the total deaths from corresponding causes, respectively. CONCLUSIONS: Long-term exposure PM1 was a novel factor hindering the life spans of people living with HIV/AIDS. Early establishment of PM1 concentration standards and efforts to achieve them will bring substantial health benefits to people living with HIV/AIDS, especially in low- and middle-income countries facing the dual challenges of high air pollution and high AIDS prevalence.

The SbbHLH041-SbEXPA11 Module Enhances Cadmium Accumulation and Rescues Biomass by Increasing Photosynthetic Efficiency in Sorghum.

In plants, expansin genes are responsive to heavy metal exposure. To study the bioremediary potential of this important gene family, we discovered a root-expressed expansin gene in sorghum, SbEXPA11, which is notably upregulated following cadmium (Cd) exposure. However, the mechanism underlying the Cd detoxification and accumulation mediated by SbEXPA11 in sorghum remains unclear. We overexpressed SbEXPA11 in sorghum and compared wild-type (WT) and SbEXPA11-overexpressing transgenic sorghum in terms of Cd accumulation and physiological indices following Cd. Compared with the WT, we found that SbEXPA11 mediates Cd tolerance by exerting reactive oxygen species (ROS)-scavenging effects through upregulating the expression of antioxidant enzymes. Moreover, the overexpression of SbEXPA11 rescued biomass production by increasing the photosynthetic efficiency of transgenic plants. In the pot experiment with a dosage of 10 mg/kg Cd, transgenic sorghum plants demonstrated higher efficacy in reducing the Cd content of the soil (8.62 mg/kg) compared to WT sorghum plants (9.51 mg/kg). Subsequent analysis revealed that the SbbHLH041 transcription factor has the ability to induce SbEXPA11 expression through interacting with the E-box located within the SbEXPA11 promoter. These findings suggest that the SbbHLH041-SbEXPA11 cascade module may be beneficial for the development of phytoremediary sorghum varieties.

Short-term exposure to ozone and mortality from AIDS-related diseases: A case-crossover study in the middle Yangtze River region, China.

BACKGROUND: Previous investigations have predominantly concentrated on the influence of ozone (O3) on general population mortality. However, a noticeable gap exists regarding the attention directed towards susceptible demographics, specifically individuals afflicted by human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS). METHODS: A dataset comprising 1467 AIDS-related fatalities from 2013 to 2020 was amassed from the Hubei Provincial Center for Disease Control and Prevention. Daily maximum 8-h average O3 levels and meteorological parameters were extracted from the ChinaHighAirPollutants dataset and the National Meteorological Science Data Center, respectively. A time-stratified case-crossover methodology was employed to scrutinize the connection between short-term exposure to O3 and AIDS-related deaths. RESULTS: A rise of one interquartile (IQR) in O3 concentration, lagged by 4 days, was associated with a 15% [95% confidence intervals (CIs): 2, 31] increase in AIDS-related deaths. Notably, males demonstrated heightened susceptibility to the adverse consequences of O3, marked by an odds ratio of 1.20 (95% CIs: 1.05, 1.37) at lag 4 day. Additionally, patients aged over 65 years exhibited escalated vulnerability to brief O3 exposure. Marriage status and educational attainment emerged as influential factors modifying the interplay between O3 and AIDS-related mortality. CONCLUSIONS: Our study presents novel evidence spotlighting the deleterious repercussions of O3 on mortality in the HIV/AIDS population.

Enhancement of the substrate specificity of D-amino acid oxidase based on tunnel-pocket engineering.

D-Amino acid oxidase (DAAO) selectively catalyzes the oxidative deamination of  D-amino acids, making it one of the most promising routes for synthesizing optically pure  L-amino acids, including  L-phosphinothricin ( L-PPT), a chiral herbicide with significant market potential. However, the native DAAOs that have been reported have low activity against unnatural acid substrate  D-PPT. Herein, we designed and screened a DAAO from Rhodotorula taiwanensis (RtwDAAO), and improved its catalytic potential toward  D-PPT through protein engineering. A semirational design approach was employed to create a mutation library based on the tunnel-pocket engineering. After three rounds of iterative saturation mutagenesis, the optimal variant M3rd -SHVG was obtained, exhibiting a >2000-fold increase in relative activity. The kinetic parameters showed that M3rd -SHVG improved the substrate binding affinity and turnover number. This is the optimal parameter reported so far. Further, molecular dynamics simulation revealed that the M3rd -SHVG reshapes the tunnel-pocket and corrects the direction of enzyme-substrate binding, allowing efficiently catalyze unnatural substrates. Our strategy demonstrates that the redesign of tunnel-pockets is effective in improving the activity and kinetic efficiency of DAAO, which provides a valuable reference for enzymatic catalysis. With the M3rd -SHVG as biocatalyst, 500 mM D, L-PPT was completely converted and the yield reached 98%. The results laid the foundation for further industrial production.

Computer-Aided Designing Peptide Inhibitors of Human Hematopoietic Prostaglandin D2 Synthase Combined Molecular Docking and Molecular Dynamics Simulation.

Human hematopoietic prostaglandin D2 synthase (HPGDS) is involved in the production of prostaglandin D2, which participates in various physiological processes, including inflammation, allergic reactions, and sleep regulation. Inhibitors of HPGDS have been investigated as potential anti-inflammatory agents. For the investigation of potent HPGDS inhibitors, we carried out a computational modeling study combining molecular docking and molecular dynamics simulation for selecting and virtual confirming the designed binders. We selected the structure of HPGDS (PDB ID: 2CVD) carrying its native inhibitor compound HQL as our research target. The random 5-mer peptide library was created by building the 3-D structure of random peptides using Rosetta Buildpeptide and performing conformational optimization. Molecular docking was carried out by accommodating the peptides into the location of their native binder and then conducting docking using FlexPepDock. The two peptides RMYYY and VMYMI, which display the lowest binding energy against HPGDS, were selected to perform a comparative study. The interaction of RMYYY and VMYMI against HPGDS was further confirmed using molecular dynamics simulation and aligned with its native binder, HQL. We show the selected binders to have stronger binding energy and more frequent interactions against HPGDS than HQL. In addition, we analyzed the solubility, hydrophobicity, charge, and bioactivity of the generated peptides, and we show that the selected strong binder may be further used as therapeutic drugs.

Extracellular Vesicles and Hypertension.

Hypertension implicates multiple organs and systems, accounting for the majority of cardiovascular diseases and cardiac death worldwide. Extracellular vesicles derived from various types of cells could transfer a variety of substances such as proteins, lipids, and nucleic acids from cells to cells, playing essential roles in both physiological and pathological processes. Extracellular vesicles are demonstrated to be closely associated with the development of essential hypertension by mediating the renin-angiotensin-aldosterone system and crosstalk between multiple vascular cells. Extracellular vesicles also participate in various kinds of pathogenesis of secondary hypertensions including acute kidney injury, renal parenchymal diseases, kidney transplantation, secretory diseases (primary aldosteronism, pheochromocytoma and paraganglioma, Cushing's syndrome), and obstructive sleep apnea. Extracellular vesicles have been proved to have the potential to be served as new biomarkers in the diagnosis, treatment, and prognosis assessment of hypertension. In the future, large multicenter cohorts are highly in demand for further verifying the sensitivity and specificity of extracellular vesicles as biomarkers.

Cobalt-catalyzed enantioselective desymmetrizing reductive cyclization of alkynyl cyclodiketones.

A highly enantioselective cobalt-catalyzed desymmetrizing reductive cyclization of alkynyl cyclodiketones has been developed. Under mild reaction conditions by employing HBpin as a reducing agent and ferrocene-based PHOX as a chiral ligand, a series of polycyclic tertiary allylic alcohols bearing contiguous quaternary stereocenters are achieved in moderate to excellent yields with excellent enantioselectivities (up to 99%). Broad substrate scope and high functional group compatibility are observed in this reaction. A CoH-catalyzed pathway involving alkyne hydrocobaltation followed by nucleophilic addition to the C[double bond, length as m-dash]O bond is proposed. Synthetic transformations of the product are conducted to demonstrate the practical utilities of this reaction.