GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs.

Small ubiquitin-like modifiers (SUMOs) are tiny but important protein regulators involved in orchestrating a broad spectrum of biological processes, either by covalently modifying protein substrates or by noncovalently interacting with other proteins. Here, we report an updated server, GPS-SUMO 2.0, for the prediction of SUMOylation sites and SUMO-interacting motifs (SIMs). For predictor training, we adopted three machine learning algorithms, penalized logistic regression (PLR), a deep neural network (DNN), and a transformer, and used 52 404 nonredundant SUMOylation sites in 8262 proteins and 163 SIMs in 102 proteins. To further increase the accuracy of predicting SUMOylation sites, a pretraining model was first constructed using 145 545 protein lysine modification sites, followed by transfer learning to fine-tune the model. GPS-SUMO 2.0 exhibited greater accuracy in predicting SUMOylation sites than did other existing tools. For users, one or multiple protein sequences or identifiers can be input, and the prediction results are shown in a tabular list. In addition to the basic statistics, we integrated knowledge from 35 public resources to annotate SUMOylation sites or SIMs. The GPS-SUMO 2.0 server is freely available at https://sumo.biocuckoo.cn/. We believe that GPS-SUMO 2.0 can serve as a useful tool for further analysis of SUMOylation and SUMO interactions.

Large-language models facilitate discovery of the molecular signatures regulating sleep and activity.

Sleep, locomotor and social activities are essential animal behaviors, but their reciprocal relationships and underlying mechanisms remain poorly understood. Here, we elicit information from a cutting-edge large-language model (LLM), generative pre-trained transformer (GPT) 3.5, which interprets 10.2-13.8% of Drosophila genes known to regulate the 3 behaviors. We develop an instrument for simultaneous video tracking of multiple moving objects, and conduct a genome-wide screen. We have identified 758 fly genes that regulate sleep and activities, including mre11 which regulates sleep only in the presence of conspecifics, and NELF-B which regulates sleep regardless of whether conspecifics are present. Based on LLM-reasoning, an educated signal web is modeled for understanding of potential relationships between its components, presenting comprehensive molecular signatures that control sleep, locomotor and social activities. This LLM-aided strategy may also be helpful for addressing other complex scientific questions.

Lactic acid bacteria with a strong antioxidant function isolated from "Jiangshui," pickles, and feces.

Excessive free radicals and iron death lead to oxidative damage, which is one of the main causes of aging and diseases. In this field of antioxidation, developing new, safe, and efficient antioxidants is the main research focus. Lactic acid bacteria (LAB) are natural antioxidants with good antioxidant activity and can regulate gastrointestinal microecological balance and immunity. In this study, 15 LAB strains from fermented foods ("Jiangshui" and pickles) or feces were evaluated in terms of their antioxidant attributes. Strains with strong antioxidant capacity were preliminarily screened by the following tests: 2,2-diphenyl-1-picrylhydrazyl (DPPH), hydroxyl radical, superoxide anion radical scavenging capacity; ferrous ion chelating assay; hydrogen peroxide tolerance capacity. Then, the adhesion of the screened strains to the intestinal tract was examined using hydrophobic and auto-aggregation tests. The safety of the strains was analyzed based on their minimum inhibitory concentration and hemolysis, and 16S rRNA was used for molecular biological identification. Antimicrobial activity tests showed them probiotic function. The cell-free supernatant of selected strains were used to explore the protective effect against oxidative damage cells. The scavenging rate of DPPH, hydroxyl radicals, and ferrous ion-chelating of 15 strains ranged from 28.81-82.75%, 6.54-68.52%, and 9.46-17.92%, respectively, the scavenging superoxide anion scavenging activity all exceeded 10%. According to all the antioxidant-related tests, strains possessing high antioxidant activities J2-4, J2-5, J2-9, YP-1, and W-4 were screened, these five strains demonstrated tolerance to 2 mM hydrogen peroxide. J2-4, J2-5, and J2-9 were Lactobacillus fermentans and γ-hemolytic (non-hemolytic). YP-1 and W-4 were Lactobacillus paracasei and α-hemolytic (grass-green hemolytic). Although L. paracasei has been proven as a safe probiotic without hemolytic characteristics, the hemolytic characteristics of YP-1 and W-4 should be further studied. Due to the weak hydrophobicity and antimicrobial activity of J2-4, finally, we selected J2-5, J2-9 for cell experiment, J2-5 and J2-9 showed an excellent ability that resistant to oxidative damage by increasing SOD, CAT, T-AOC activity of 293T cells. Therefore, J2-5, and J2-9 strains from fermented foods "Jiangshui" could be used as potential antioxidants for functional food, health care, and skincare.

GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins.

Protein phosphorylation, catalyzed by protein kinases (PKs), is one of the most important post-translational modifications (PTMs), and involved in regulating almost all of biological processes. Here, we report an updated server, Group-based Prediction System (GPS) 6.0, for prediction of PK-specific phosphorylation sites (p-sites) in eukaryotes. First, we pre-trained a general model using penalized logistic regression (PLR), deep neural network (DNN), and Light Gradient Boosting Machine (LightGMB) on 490 762 non-redundant p-sites in 71 407 proteins. Then, transfer learning was conducted to obtain 577 PK-specific predictors at the group, family and single PK levels, using a well-curated data set of 30 043 known site-specific kinase-substrate relations in 7041 proteins. Together with the evolutionary information, GPS 6.0 could hierarchically predict PK-specific p-sites for 44046 PKs in 185 species. Besides the basic statistics, we also offered the knowledge from 22 public resources to annotate the prediction results, including the experimental evidence, physical interactions, sequence logos, and p-sites in sequences and 3D structures. The GPS 6.0 server is freely available at https://gps.biocuckoo.cn. We believe that GPS 6.0 could be a highly useful service for further analysis of phosphorylation.

Structure-Based Virtual Screening of Helicobacter pylori SecA Inhibitors.

The human bacterial pathogen Helicobacter pylori causes a range of gastric diseases. The killing rate of Helicobacter pylori is declining year by year because of high antibiotics resistance. It is urgent to develop new target and novel anti- Helicobacter pylori drugs. As an "energy pump" for bacterial cells, SecA is essential for bacterial growth and drives bacterial protein transmembrane transport, moreover SecA is absent in mammals, all of which nominate SecA as an attractive antimicrobial target. Here, we provided a structure-based virtual screening method to screen the 3D-diversity natural-product-like screening library against SecA for novel anti- Helicobacter pylori inhibitors with novel scaffolds. In this study, homology modeling was used to construct the three-dimensional structure of Helicobacter pylori SecA. Two rounds of molecular docking were then used to find new small-molecule inhibitors of SecA, identifying six lead candidates that maintained key interactions with the binding pocket. After that, molecular dynamics simulations were used to explore more accurate ligand-receptor binding modes in states close to natural conditions. Encouragingly, all six compounds were relatively stable during the simulation. Apart from that the binding free energy calculation based on MM/PBSA demonstrated favorable results of < -13.642 kcal/mol. Finally, ADME-T analysis indicated that these compounds were also sufficiently druggable. All six compounds can be well combined with the crystal structure, which further facilitate the development of SecA inhibitors and lead compounds against Helicobacter pylori.

Towards precision medicine: Omics approach for COVID-19.

The coronavirus disease 2019 (COVID-19) pandemic had a devastating impact on human society. Beginning with genome surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the development of omics technologies brought a clearer understanding of the complex SARS-CoV-2 and COVID-19. Here, we reviewed how omics, including genomics, proteomics, single-cell multi-omics, and clinical phenomics, play roles in answering biological and clinical questions about COVID-19. Large-scale sequencing and advanced analysis methods facilitate COVID-19 discovery from virus evolution and severity risk prediction to potential treatment identification. Omics would indicate precise and globalized prevention and medicine for the COVID-19 pandemic under the utilization of big data capability and phenotypes refinement. Furthermore, decoding the evolution rule of SARS-CoV-2 by deep learning models is promising to forecast new variants and achieve more precise data to predict future pandemics and prevent them on time.

Nutrient and Maillard reaction product concentrations of commercially available pet foods and treats.

Thermal processing is used to produce most commercial pet foods and treats to improve safety, shelf life, nutritional characteristics, texture, and nutrient digestibility. However, heat treatments can degrade protein quality by damaging essential amino acids, as well as contribute to the Maillard reaction. The Maillard reaction forms melanoidins that favorably improve food qualities (e.g., color, flavor, aroma), but also form Maillard reaction products (MRP) and advanced glycation end-products that may negatively affect health. Because commercial pet diets are frequently fed to domestic cats and dogs throughout their lifetimes, it is critical to quantify MRP concentrations and understand the variables that influence their formation so future diets may be formulated with that in mind. Because few research studies on MRP in pet diets have been conducted, the goals of this study were to measure the MRP in commercial pet foods and treats, estimate pet MRP intake, and correlate MRP with dietary macronutrient concentrations. Fifty-three dry and wet dog foods, dog treats, and cat foods were analyzed for dry matter, organic matter, crude protein, acid-hydrolyzed fat, total dietary fiber, and gross energy using standard techniques. MRP were analyzed using high-performance liquid chromatography and gas chromatography-mass spectrometry. Data were analyzed using the Mixed Models procedure of SAS 9.4. Dry foods had lower reactive lysine concentrations and reactive lysine: total lysine ratios (indicator of damage) than wet foods. Wet foods had more fructoselysine (FRUC) than dry foods; however, dry dog treats contained more FRUC than wet dog treats. The greatest 5-hydroxymethyl-2-furfural (HMF) concentrations were measured in dry and wet dog foods, whereas the lowest HMF concentrations were measured in dry and wet cat foods. Based on dietary concentrations and estimated food intakes, dogs and cats fed wet foods are more likely to consume higher carboxymethyllysine and FRUC concentrations than those fed dry foods. However, dogs fed wet foods are more likely to consume higher HMF concentrations than those fed dry foods. In cats, those fed dry foods would consume higher HMF concentrations than those fed wet foods. We demonstrated that pet foods and treats contain highly variable MRP concentrations and depend on diet/treat type. In general, higher MRP concentrations were measured in wet pet foods and dry treats. While these findings are valuable, in vivo testing is needed to determine if and how MRP consumption affect pet health.

When heat is applied to food, the structure of sugars and proteins are rearranged. Some of the newly formed compounds are Maillard reaction products (MRP). The Maillard reaction can form melanoidins that improve color, flavor, and aroma, but can also lead to the loss of essential amino acids and the formation of advanced glycation end-products that may negatively affect animal health. Most commercial pet foods and treats are heated to improve safety, shelf life, nutritional characteristics, texture, and nutrient digestion, but MRP formation can be a problem. Because commercial pet foods are fed to domestic cats and dogs throughout their entire lives, quantifying MRP and understanding the variables that influence their formation is critical. The goals of this study were to determine the amount of MRP in commercial pet foods and treats, estimate MRP ingestion in pets, and correlate MRP with dietary macronutrient concentrations. Wet foods and dry treats contained more fructoselysine than dry foods, while dry foods contained more 5-hydroxymethyl-2-furfural. According to our findings, wet diets will result in higher total MRP, carboxymethyllysine, and fructoselysine intake than dry diets. While these findings are valuable, in vivo testing is needed to determine if and how MRP consumption affect pet health.

EXPERT: transfer learning-enabled context-aware microbial community classification.

Microbial community classification enables identification of putative type and source of the microbial community, thus facilitating a better understanding of how the taxonomic and functional structure were developed and maintained. However, previous classification models required a trade-off between speed and accuracy, and faced difficulties to be customized for a variety of contexts, especially less studied contexts. Here, we introduced EXPERT based on transfer learning that enabled the classification model to be adaptable in multiple contexts, with both high efficiency and accuracy. More importantly, we demonstrated that transfer learning can facilitate microbial community classification in diverse contexts, such as classification of microbial communities for multiple diseases with limited number of samples, as well as prediction of the changes in gut microbiome across successive stages of colorectal cancer. Broadly, EXPERT enables accurate and context-aware customized microbial community classification, and potentiates novel microbial knowledge discovery.

Effect of Myrcene on Th17/Treg Balance and Endocrine Function in Autoimmune Premature Ovarian Insufficiency Mice through the MAPK Signaling Pathway.

BACKGROUND: Premature ovarian insufficiency (POI) is a defect of ovarian functions in women younger than 40 years old. Although a large number of studies have focused on investigating autoimmune POI, its detailed pathogenesis is still largely unknown. Several studies have indicated that Myrcene exerted a part in the biological processes of various diseases. Nonetheless, whether Myrcene could influence the development of autoimmune POI remains to be elucidated. METHODS: POI model was established by injecting zona pellucida glycoprotein 3 (pZP3). Hematoxylin and eosin (H&E) staining was applied to evaluate the pathological features of ovarian tissues. Enzymelinked immunosorbent assay (ELISA) was used for assessing the concentrations of estradiol (E2), follicle-stimulating hormone (FSH), luteinizing hormone (LH), anti-Müllerian hormone (AMH) and interleukin (IL)-17. Flow cytometry analysis was conducted for assessing the balance of Th17/Treg cells. RESULTS: The results showed that decreased levels of body weight, ovarian weight and ovarian index were reversed by Myrcene in POI model mice. The estrous cycles in mice were extended in pZP3 mice and Myrcene administration restored it to normal. The reduced number of primordial, primary, and secondary follicles as well as the increased number of atretic follicles in POI mice were offset by Myrcene administration. Moreover, Myrcene could modulate the Th17/Treg balance in autoimmune POI. Besides, Myrcene suppressed the MAPK signaling pathway in pZP3 mice. CONCLUSION: Myrcene regulated the Th17/Treg balance and endocrine function in autoimmune POI mice through the MAPK signaling pathway, which might provide a reference for improving the treatment of autoimmune POI.

Promising natural products against SARS-CoV-2: Structure, function, and clinical trials.

The corona virus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus type 2 (SARS-COV-2) poses a severe threat to human health and still spreads globally. Due to the high mutation ratio and breakthrough infection rate of the virus, vaccines and anti-COVID-19 drugs require continual improvements. Drug screening research has shown that some natural active products can target the critical proteins of SARS-CoV-2, including 3CLpro, ACE2, FURIN, and RdRp, which could produce great inhibitory effects on SARS-COV-2. In addition, some natural products have displayed activities of immunomodulation, antiinflammatory, and antihepatic failure in COVID-19 clinical trials, which may relate to their non-monomeric structures. However, further evaluation and high-quality assessments, including safety verification tests, drug interaction tests, and clinical trials, are needed to substantiate natural products' multi-target and multi-pathway effects on COVID-19. Here, we review the literature on several promising active natural products that may act as vaccine immune enhancers or provide targeted anti-COVID-19 drugs. The structures, mechanisms of action, and research progress of these natural products are analyzed, to hopefully provide effective ideas for the development of targeted drugs that possess better structure, potency, and safety.

HemI 2.0: an online service for heatmap illustration.

Recent high-throughput omics techniques have produced a large amount of biological data. Visualization of big omics data is essential to answer a wide range of biological problems. As a concise but comprehensive strategy, a heatmap can analyze and visualize high-dimensional and heterogeneous biomolecular expression data in an attractive artwork. In 2014, we developed a stand-alone software package, Heat map Illustrator (HemI 1.0), which implemented three clustering methods and seven distance metrics for heatmap illustration. Here, we significantly improved 1.0 and released the online service of HemI 2.0, in which 7 clustering methods and 22 types of distance metrics were implemented. In HemI 2.0, the clustering results and publication-quality heatmaps can be exported directly. For an in-depth analysis of the data, we further added an option of enrichment analysis for 12 model organisms, with 15 types of functional annotations. The enrichment results can be visualized in five idioms, including bubble chart, bar graph, coxcomb chart, pie chart and word cloud. We anticipate that HemI 2.0 can be a helpful web server for visualization of biomolecular expression data, as well as the additional enrichment analysis. HemI 2.0 is freely available for all users at: https://hemi.biocuckoo.org/.

MSC-ACE2 Ameliorates Streptococcus uberis-Induced Inflammatory Injury in Mammary Epithelial Cells by Upregulating the IL-10/STAT3/SOCS3 Pathway.

In the dairy industry, Streptococcus uberis (S. uberis) is one of the most important pathogenic bacteria associated with mastitis in milk-producing cows, causing vast economic loss. To date, the only real effective method of treating and preventing streptococcal mastitis is antimicrobial therapy. In many inflammatory diseases, mesenchymal stem cells (MSCs) and angiotensin-converting enzyme 2 (ACE2) play an anti-inflammatory and anti-injurious role. Accordingly, we hypothesized that MSCs overexpressing ACE2 (MSC-ACE2) would ameliorate the inflammatory injury caused by S. uberis in mammary epithelial cells more efficiently than MSC alone. By activating the transcription 3/suppressor of cytokine signaling 3 (IL-10/STAT3/SOCS3) signaling pathway, MSC-ACE2 inhibited the NF-κB, MAPKs, apoptosis, and pyroptosis passways. Moreover, MSC-ACE2 overturned the downregulation of Occludin, Zonula occludens 1 (ZO-1), and Claudin-3 expression levels caused by S. uberis, suggesting that MSC-ACE2 promotes the repair of the blood-milk barrier. MSC-ACE2 demonstrated greater effectiveness than MSC alone, as expected. Based on these results, MSC-ACE2 effectively inhibits EpH4-Ev cell's inflammatory responses induced by S. uberis, and would be an effective therapeutic tool for treating streptococcal mastitis.

[Cultivation of college students' innovative and entrepreneurial thinking and ability based on Synthetic Biology and iGEM].

Synthetic Biology is one of the most promising fields of modern Biology and a frontier interdisciplinary subject in the 21st century. With the rapid development of synthetic biology, the International Genetically Engineered Machine (iGEM) competition has emerged. The iGEM competition, based on the subject foundation of Synthetic Biology, intends to solve the biological problems in our daily life by applying modern biological technology. In recent years, with the continuous increase of participating teams, the iGEM competition has received extensive attention and achieved great progress. On the basis of the development of Synthetic Biology, we analyzed the 2018-2020 award-winning projects of the iGEM competition and illustrated the role and significance of the iGEM competition in cultivating college students' innovative thinking and ability with the participation experience of the iGEM team of Southwest Jiaotong University as an example.

Erianin suppresses proliferation and migration of cancer cells in a pyruvate carboxylase-dependent manner.

Erianin is a natural small molecule dibenzyl compound extracted from Dendrobium officinale or Dendrobium chrysotoxum. Studies show erianin has many pharmacological functions such as antioxidant, antibacterial, antiviral, improving diabetic nephropathy, relaxing bronchial smooth muscle and anti-tumor. However, the erianin-mediated molecular mechanism is elusive, and the target protein of erianin is not clear yet. Here, we screened and identified that the target protein of erianin in human hepatoma HepG2 cells is human pyruvate carboxylase, and explored the anti-tumor signal pathway regulated by erianin in several cell lines. Firstly, the interaction between human pyruvate carboxylase and erianin was studied by bioinformatics and biochemical methods. Secondly, in vitro, erianin can specifically inhibit the activity of human pyruvate carboxylase, and the purified human pyruvate carboxylase can specifically bind to the activity probe of erianin. Thirdly, human pyruvate carboxylase is highly expressed in a variety of malignant tumors, and the inhibitory effect of erianin on tumor cells is positively correlated with the expression of human pyruvate carboxylase, and erianin can selectively inhibit the activity of pyruvate carboxylase. Finally, erianin can regulate the pyruvate carboxylase-mediated Wnt/ ß- Catenin pathway. All of which provide important data for the further study of the anticancer mechanism of erianin, and lay a solid foundation for the further development and utilization of erianin.

lncRNA CDKN2A-AS1 facilitates tumorigenesis and progression of epithelial ovarian cancer via modulating the SOSTDC1-mediated BMP-SMAD signaling pathway.

Ovarian cancer (OC) is the fifth most common female malignant tumor and the leading cause of cancer-related death in women worldwide. Epithelial ovarian cancer (EOC) is the predominant type of OC. Investigating the mechanism underlying tumorigenesis and progression of EOC is urgent. Our previous research has shown that long non-coding RNAs (lncRNAs) CDKN2A-AS1 is upregulated in EOC tissues and cells. Furthermore, we have predicted that CDKN2A-AS1 is associated with the bone morphogenetic protein (BMP)-SMAD signaling pathway, which is negatively regulated by the sclerostin domain containing 1 (SOSTDC1). Therefore, we conjecture that the CDKN2A-AS1 regulate BMP-SMAD signaling pathway via interacting with SOSTDC1, which need more investigation. Moreover, the functions of the BMP-SMAD signaling pathway and the SOSTDC1 on EOC are still unclear. Herein, we unearthed that CDKN2A-AS1, BMP2/4/7, SMAD1/5/9 and phosphorylation of SMAD1/5/9 (p-SMAD1/5/9) were upregulated in EOC tissues and cells, whereas SOSTDC1 was downregulated in EOC tissues and cells. We firstly demonstrated that CDKN2A-AS1 bound directly with the SOSTDC1. CDKN2A-AS1 downregulated the expression of SOSTDC1, but upregulated the expression of BMP2/4/7, SMAD1/5/9, and p-SMAD1/5/9. CDKN2A-AS1 promoted the proliferation, migration, invasion of EOC cells and tumor growth in vivo, whereas SOSTDC1 inhibited the proliferation, migration, invasion of EOC cells. Knockdown SOSTDC1 rescued the inhibitory effect of si-lncRNA CDKN2A-AS1 on the EOC cells proliferation, migration and invasion. These results demonstrated that CDKN2A-AS1activated the BMP-SMAD signaling pathway by directly bind with SOSTDC1 to promote EOC tumor growth. CDKN2A-AS1/SOSTDC1 axis may provide a novel therapeutic strategy for EOC treatment.

A bibliometric analysis and visualization of photothermal therapy on cancer.

BACKGROUND: Cancer is one of the most lethal diseases in the world, and photothermal therapy was reported recently as a new and effective therapy for cancer. This study offers the bibliometric and visualization analysis of photothermal therapy on cancer. METHODS: A record of 6,233 papers in this field from 1995 to 2019 was obtained based on the Web of Science Core Collection (WoSCC). And CiteSpace was used to analyze the annual trends of publications, countries, institutions, journals, co-cited references, and keywords in the field of photothermal therapy on cancer. RESULTS: We identified that the number of publications continually increased over the time. The most productive country and institution in this field was China and Chinese Academy of Sciences, respectively. The ACS Appl Mater Interfaces was the most active journal. Co-cited references analysis revealed the top landmark articles in the field. Co-occurrence keywords and their clustered network were analyzed, revealing that materials, especially nanomaterials, used in photothermal therapy, remained the hotspots in this research field. Timezone view and burst detection of keywords showed that nanomaterials were always the hotspots and the frontier topics in this field. CONCLUSIONS: The current study revealed that photothermal therapy has become a subject of growing study and a very important research area. In addition, the research of materials in photothermal therapy, especially nanomaterials, which were applied in photothermal therapy to treat cancer effectively, is the foci and the frontier topic in this field.

Inactivation of Wnt-LRP5 signaling suppresses the proliferation and migration of ovarian cancer cells.

BACKGROUND: Ovarian cancer (OCa) is the most lethal gynecological malignant tumor, with few or no specific symptoms in its early stage. There are many signaling pathways involved in the process of OCa progression, among which the highly complex Wnt signaling pathway plays a unique role in the occurrence and development of OCa because of its functions of regulating gene expression, cell proliferation, migration, and invasion. Lipoprotein associated receptor protein 5/6 (LRP5/6) binds to activate this key pathway. Therefore, it is very important to study the mechanism of Wnt-LRP5 signaling pathway in the proliferation and migration of OCa. METHODS: In the present study, we have investigated the role of Wnt-LRP5 signaling pathway in OCa proliferation and migration for the first time using the dominant negative plasmid of LRP5 (DN-LRP5) and human OCa cells HO8910PM plus in a mouse model. RESULTS: Our data showed inactivation of LRP5 resulted in shift of epithelial-mesenchymal transition (EMT), rearrangement of the cytoskeleton, lowered activity of pro-proliferation and pro-migration cancer signaling pathways including Akt, p38 and NF-κB, eventually decreased proliferation and migration of OCa cells HO8910PM in vitro. Moreover, in vivo OCa-DN-LRP5 mouse model developed significantly smaller tumors as determined by inoculation of HO8910PM-DN-LRP5 cells into nude mice. CONCLUSIONS: Collectively, our results demonstrate the dominant role of Wnt-LRP5 in OCa proliferation and migration and its potential as a valuable therapeutic target.

SARS-CoV-2 and SARS-CoV: Virtual screening of potential inhibitors targeting RNA-dependent RNA polymerase activity (NSP12).

Since the outbreak of severe acute respiratory syndrome (SARS) in 2003, the harm caused by coronaviruses to the world cannot be underestimated. Recently, a novel coronavirus (severe acute respiratory syndrome coronavirus-2 [SARS-CoV-2]) initially found to trigger human severe respiratory illness in Wuhan City of China in 2019, has infected more than six million people worldwide by 21 June 2020, and which has been recognized as a public health emergency of international concern as well. And the virus has spread to more than 200 countries around the world. However, the effective drug has not yet been officially licensed or approved to treat SARS-Cov-2 and SARS-Cov infection. NSP12-NSP7-NSP8 complex of SARS-CoV-2 or SARS-CoV, essential for viral replication and transcription, is generally regarded as a potential target to fight against the virus. According to the NSP12-NSP7-NSP8 complex (PDB ID: 7BW4) structure of SARS-CoV-2 and the NSP12-NSP7-NSP8 complex (PDB ID: 6NUR) structure of SARS-CoV, NSP12-NSP7 interface model, and NSP12-NSP8 interface model were established for virtual screening in the present study. Eight compounds (Nilotinib, Saquinavir, Tipranavir, Lonafarnib, Tegobuvir, Olysio, Filibuvir, and Cepharanthine) were selected for binding free energy calculations based on virtual screening and docking scores. All eight compounds can combine well with NSP12-NSP7-NSP8 in the crystal structure, providing drug candidates for the treatment and prevention of coronavirus disease 2019 and SARS.

Predicting the Animal Susceptibility and Therapeutic Drugs to SARS-CoV-2 Based on Spike Glycoprotein Combined With ACE2.

Recently, a few animals have been frequently reported to have been diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Whether they are SARS-CoV-2 intermediate hosts is worthy of great attention. The interaction of SARS-CoV-2 spike protein and its acceptor protein ACE2 is an important issue in determining viral host range and cross-species infection, while the binding capacity of Spike protein to ACE2 of different species is unknown. Here, we used the atomic structure model of SARS-CoV-2 and human ACE2 to assess the receptor utilization capacity of ACE2s from 10 kinds of animals. Results show that chimpanzees, domestic cats and cattles are more susceptible to infection by SARS-CoV-2. Cats in particular, such as pet cats and stray cats, interact very closely with humans, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic. Furthermore, based on ACE2(cats)-SARS-CoV-2-RBD model, through high-throughput screening methods using a pool of 30,000 small molecules, eight compounds were selected for binding free energy calculations. All the eight compounds can effectively interfere with the binding of ACE2 and Spike protein, especially Nelfinavir, providing drug candidates for the treatment and prevention of SARS-CoV-2, suggesting further assessment of the anti-SARS-CoV-2 activity of these compounds in cell culture. Although we only reported the results of the simulation, and more laboratory and epidemiological investigation are required. Like cats are a risk factor, we can further detect SARS-CoV-2 according to the susceptibility of different animals, find the potential host of infection, and completely cut off the living space of the virus. Especially, cats could be a choice of animal model for screening antiviral drugs or vaccine candidates against SARS-CoV-2.

Synergistic Effects from Combination of Cryptotanshinone and Fosfomycin Against Fosfomycin-Susceptible and Fosfomycin-Resistant Staphylococcus aureus.

PURPOSE: Fosfomycin is now widely used to treat methicillin-resistant S. aureus due to its unique antibacterial activity. However, fosfomycin-resistant S. aureus has rapidly emerged, it is urgent to find new treatments to eliminate fosfomycin-resistant S. aureus infection. The purpose of this study was to analyze the activity of cryptanshinone, a traditional Chinese medicine monomer, in combination with fosfomycin against fosfomycin-sensitive S. aureus (FSSA) and fosfomycin-resistant S. aureus (FRSA). METHODS: The MICs of fosfomycin and/or cryptanshinone were determined by agar dilution assay and checkerboard microdilution assay. Furthermore, synergistic effects from fosfomycin and/or cryptanshinone were analyzed by the time-kill assay in vitro. RESULTS: The combination of fosfomycin and cryptotanshinone had a synergistic effect on most (71.43%) of the FRSA and had a partial (28.57%) synergistic effect on a small part. In addition, time sterilization curve verified synergistic activity between cryptanshinone and fosfomycin against FSSA and FRSA, especially when fosfomycin was added for a second time. CONCLUSION: These data suggest that cryptanshinone combined with fosfomycin could be a novel treatment for FRSA and provide a new direction for the treatment of bacterial infections in the future.