Temporal transcriptome and metabolome study revealed molecular mechanisms underlying rose responses to red spider mite infestation and predatory mite antagonism.

Introduction: Red spider mite (Tetranychus urticae) infestation (SMI) is a detrimental factor for roses grown indoors. Although predatory mite (Neoseiulus californicus) antagonism (PMA) is often utilized to alleviate SMI damage, little is known about the defensive response of greenhouse-grown roses to SMI and the molecular mechanism by which PMA protects roses. Methods: To determine the transcriptome and metabolome responses of roses to SMI and PMA, the leaves of a rose cultivar ("Fairy Zixia/Nightingale") were infested with T. urticae, followed by the introduction of predator mite. Leaf samples were collected at various time points and subjected to transcriptome and metabolome analyses. Results: We found that 24 h of SMI exerted the most changes in the expression of defense-related genes and metabolites in rose leaves. KEGG pathway analysis of differentially expressed genes (DEGs) and metabolites revealed that rose responses to SMI and PMA were primarily enriched in pathways such as sesquiterpenoid and triterpenoid biosynthesis, benzoxazinoid biosynthesis, stilbenoid, diarylheptanoid and gingerol biosynthesis, phytosterol biosynthesis, MAPK signaling pathway, phenylpropanoid biosynthesis, and other pathways associated with resistance to biotic stress. Rose reacted to SMI and PMA by increasing the expression of structural genes and metabolite levels in phytosterol biosynthesis, mevalonate (MVA) pathway, benzoxazinoid biosynthesis, and stilbenoid biosynthesis. In addition, PMA caused a progressive recover from SMI, allowing rose to revert to its normal growth state. PMA restored the expression of 190 essential genes damaged by SMI in rose leaves, including transcription factors DRE1C, BH035, MYB14, EF110, WRKY24, NAC71, and MY108. However, after 144 h of PMA treatment, rose responsiveness to stimulation was diminished, and after 192 h, the metabolic levels of organic acids and lipids were recovered in large measure. Conclusion: In conclusion, our results offered insights on how roses coordinate their transcriptome and metabolome to react to SMI and PMA, therefore shedding light on how roses, T. urticae, and N. californicus interact.

IAA Synthesis Pathway of Fitibacillus barbaricus WL35 and Its Regulatory Gene Expression Levels in Potato (Solanum tuberosum L.).

Indole-3-acetic acid (IAA), as an important regulator of potato growth, seriously affects the growth and yield of potato. Although many studies have reported that IAA-producing Bacillus can promote plant growth, little research has been conducted on its synthesis pathway and molecular mechanisms. In this study, an IAA-producing strain WL35 was identified as Fitibacillus barbaricus, and its yield was 48.79 mg·L-1. The results of the pot experiments showed that WL35 significantly increased plant height, stem thickness, chlorophyll content, and number of leaves of potato plants by 31.68%, 30.03%, 32.93%, and 36.59%, respectively. In addition, in the field experiments, WL35-treated plants increased commercial potato yield by 16.45%, vitamin C content by 16.35%, protein content by 75%, starch content by 6.60%, and the nitrogen, phosphorus, and potassium accumulation by 9.98%, 12.70%, and 26.76%, respectively. Meanwhile, the synthetic pathway of WL35 was found to be dominated by the tryptophan-dependent pathway, the IAM, TAM, and IPA pathways worked together, and the pathways that played a role at different times were different. Furthermore, RNA-seq analysis showed that there were a total of 2875 DEGs regulated in the samples treated with WL35 seed dressing compared with the CK, of which 1458 genes were up-regulated and 1417 genes were down-regulated. Potato roots express differential genes enriched in processes such as carbohydrate metabolism processes and cellular polysaccharide metabolism, which regulate potato plant growth and development. The above results provide a theoretical basis for the further exploration of the synthesis pathway of IAA and its growth-promoting mechanism in potato.

Bacillus velezensis Y6, a Potential and Efficient Biocontrol Agent in Control of Rice Sheath Blight Caused by Rhizoctonia solani.

Rice sheath blight is a serious disease caused by Rhizoctonia solani that reduces rice yield. Currently, there is a lack of efficient and environmentally friendly control methods. In this study, we found that Bacillus velezensis (B. velezensis) Y6 could significantly inhibit the growth of mycelium in Rhizoctonia solani, and its control efficiency against rice sheath blight was 58.67% (p < 0.01) in a pot experiment. Lipopeptides play an important role in the control of rice sheath blight by B. velezensis Y6, among which iturin and fengycin are essential, and iturin W, a novel lipopeptide in B. velezensis, plays a major role in lipopeptide antagonism to Rhizoctonia solani. In the field, we also found that inoculation with B. velezensis Y6 can increase rice yield (dry weight) by 11.75%. Furthermore, the transcriptome profiling results of the rice roots revealed that there were a total of 1227 differential genes (DEGs) regulated when treated with Y6, of which 468 genes were up-regulated and 971 genes were down-regulated in rice roots compared with the control. Among them, the DEGs were mainly distributed in biological processes (BP) and were mainly enriched in response to stimulus (GO:0050896), response to stress (GO:0006950), and response to abiotic stimulus (GO:0009628). According to the KEGG pathway analysis, there were 338 DEGs classified into 87 KEGG functional pathway categories. Compared with the control, a large number of enriched genes were distributed in phenylpropanoid biosynthesis (map00940), glutathione metabolism (map00480), glycolysis/gluconeogenesis (map00010), and amino sugar and nucleotide sugar metabolism (map00520). In summary, this investigation provides a new perspective for studying the molecular mechanism of B. velezensis in controlling rice sheath blight.

Identification of novel covalent JAK3 inhibitors through consensus scoring virtual screening: integration of common feature pharmacophore and covalent docking.

Accumulated research strongly indicates that Janus kinase 3 (JAK3) is intricately involved in the initiation and advancement of a diverse range of human diseases, underscoring JAK3 as a promising target for therapeutic intervention. However, JAK3 shows significant homology with other JAK family isoforms, posing substantial challenges in the development of JAK3 inhibitors. To address these limitations, one strategy is to design selective covalent JAK3 inhibitors. Therefore, this study introduces a virtual screening approach that combines common feature pharmacophore modeling, covalent docking, and consensus scoring to identify novel inhibitors for JAK3. First, common feature pharmacophore models were constructed based on a selection of representative covalent JAK3 inhibitors. The optimal qualitative pharmacophore model proved highly effective in distinguishing active and inactive compounds. Second, 14 crystal structures of the JAK3-covalent inhibitor complex were chosen for the covalent docking studies. Following validation of the screening performance, 5TTU was identified as the most suitable candidate for screening potential JAK3 inhibitors due to its higher predictive accuracy. Finally, a virtual screening protocol based on consensus scoring was conducted, integrating pharmacophore mapping and covalent docking. This approach resulted in the discovery of multiple compounds with notable potential as effective JAK3 inhibitors. We hope that the developed virtual screening strategy will provide valuable guidance in the discovery of novel covalent JAK3 inhibitors.

Biological Control of Avocado Branch Blight Caused by Lasiodiplodia theobromae Using Bacillus velezensis.

In recent years, avocado branch blight has gradually become one of the major diseases causing mortality of avocado trees, which seriously affects the economic development of avocado planting regions. In order to investigate the cause of the disease, the pathogens were isolated from the interroot of avocado trees with the onset of the disease and identified as Lasiodiplodia theobromae. At the same time, three Bacillus velezensis strains, YK194, YK201, and YK268, with better antagonistic effects and high stability against L. theobromae, were isolated from the rhizospheric soil of healthy avocado plants. The results of branch experiments and field trials showed that the avocado leaves as well as branches treated with the strains YK194, YK201, and YK268 did not develop disease, and the incidence of avocado trees was significantly reduced. In the branch experiments, the biological control effect of the strains YK194, YK201, and YK268 reached 62.07, 52.70, and 72.45%, respectively. In the field experiments, it reached 63.85, 63.43, and 73.86%, respectively, which indicated that all these three strains possessed good biological control effects on avocado branch blight. Further investigation on the mechanism of action of antagonistic strains revealed that B. velezensis YK268 could produce lipopeptides, namely, surfactin, fengycin, and iturin, which could significantly inhibit the spore germination of L. theobromae. Consequently, these three isolates have potential as biocontrol agents against L. theobromae.

Optimization of virtual screening against phosphoinositide 3-kinase delta: Integration of common feature pharmacophore and multicomplex-based molecular docking.

Extensive research has accumulated which suggests that phosphatidylinositol 3-kinase delta (PI3Kδ) is closely related to the occurrence and development of various human diseases, making PI3Kδ a highly promising drug target. However, PI3Kδ exhibits high homology with other members of the PI3K family, which poses significant challenges to the development of PI3Kδ inhibitors. Therefore, in the present study, a hybrid virtual screening (VS) approach based on a ligand-based pharmacophore model and multicomplex-based molecular docking was developed to find novel PI3Kδ inhibitors. 13 crystal structures of the human PI3Kδ-inhibitor complex were collected to establish models. The inhibitors were extracted from the crystal structures to generate the common feature pharmacophore. The crystallographic protein structures were used to construct a naïve Bayesian classification model that integrates molecular docking based on multiple PI3Kδ conformations. Subsequently, three VS protocols involving sequential or parallel molecular docking and pharmacophore approaches were employed. External predictions demonstrated that the protocol combining molecular docking and pharmacophore resulted in a significant improvement in the enrichment of active PI3Kδ inhibitors. Finally, the optimal VS method was utilized for virtual screening against a large chemical database, and some potential hit compounds were identified. We hope that the developed VS strategy will provide valuable guidance for the discovery of novel PI3Kδ inhibitors.

Biological control of potato common scab and growth promotion of potato by Bacillus velezensis Y6.

Potato common scab, caused mainly by Streptomyces scabies, causes surface necrosis and reduces the economic value of potato tubers, but effective chemical control is still lacking. In this study, an attempt was made to control potato common scab by inoculating potatoes with Bacillus velezensis (B. velezensis) and to further investigate the mechanism of biological control. The results showed that B. velezensis Y6 could reduce the disease severity of potato common scab from 49.92 ± 25.74% [inoculated with Streptomyces scabies (S. scabies) only] to 5.56 ± 1.89% (inoculated with S. scabies and Y6 on the same day) and increase the potato yield by 37.32% compared with the control under pot experiment in this study. Moreover, in the field trial, it was found that Y6 could also significantly reduce disease severity from 13.20 ± 1.00% to 4.00 ± 0.70% and increase the potato yield from 2.07 ± 0.10 ton/mu to 2.87 ± 0.28 ton/mu (p < 0.01; Tukey's test). Furthermore, RNA-seq analysis indicated that 256 potato genes were upregulated and 183 potato genes were downregulated in response to B. velezensis Y6 inoculation. In addition, strain Y6 was found to induce the expression of plant growth-related genes in potato, including cell wall organization, biogenesis, brassinosteroid biosynthesis, and plant hormone transduction genes, by 1.01-4.29 times. As well as up-regulate hydroquinone metabolism-related genes and several transcription factors (bHLH, MYB, and NAC) by 1.13-4.21 times. In summary, our study will help to understand the molecular mechanism of biological control of potato common scab and improve potato yield.

Evaluation of the anti-inflammatory effects of PI3Kδ/γ inhibitors for treating acute lung injury.

Phosphatidylinositol 3-kinase delta (PI3Kδ) and gamma (PI3Kγ) are predominantly located in immune and hematopoietic cells. It is well-established that PI3Kδ/γ plays important roles in the immune system and participates in inflammation; hence, it could be a potential target for anti-inflammatory therapy. Currently, several PI3K inhibitors are used clinically to treat cancers with aberrant PI3K signaling; however, their role in treating acute respiratory inflammatory diseases has rarely been explored. Herein, we investigated the potential anti-inflammatory activities of several pharmacological PI3K inhibitors, including marketed drugs idelalisib (PI3Kδ), duvelisib (PI3Kδ/γ), and copanlisib (pan-PI3K with preferential α/δ) and the clinical drug eganelisib (PI3Kγ), for treating acute lung injury (ALI). In the lipopolysaccharide-induced RAW264.7 macrophage inflammatory model, the four inhibitors significantly suppressed proinflammatory cytokine expression by inhibiting the PI3K signaling pathway. Oral administration of PI3K inhibitors markedly improved lung injury in a murine model of ALI. PI3K pathway inhibition decreased inflammatory cell infiltration and totalprotein levels, as well as reduced the expression of associated lung inflammatory factors. Collectively, all four representative PI3K inhibitors exerted prominent anti-inflammatory properties, indicating that PI3K δ and/or γ inhibition could be ideal targets to treat respiratory inflammatory diseases by reducing the inflammatory response. The findings of the current study provide a new basis for utilizing PI3K inhibitors to treat acute respiratory inflammatory diseases.

Betaine-Based and Polyguanidine-Inserted Zwitterionic Micelle as a Promising Platform to Conquer the Intestinal Mucosal Barrier.

Developing nanocarriers for oral drug delivery is often hampered by the dilemma of balancing mucus permeation and epithelium absorption, since huge differences in surface properties are required for sequentially overcoming these two processes. Inspired by mucus-penetrating viruses that universally possess a dense charge distribution with equal opposite charges on their surfaces, we rationally designed and constructed a poly(carboxybetaine)-based and polyguanidine-inserted cationic micelle platform (hybrid micelle) for oral drug delivery. The optimized hybrid micelle exhibited a great capacity for sequentially overcoming the mucus and villi barriers. It was demonstrated that a longer zwitterionic chain was favorable for mucus diffusion for hybrid micelles but not conducive to cellular uptake. In addition, the significantly enhanced internalization absorption of hybrid micelles was attributed to the synergistic effect of polyguanidine and proton-assisted amine acid transporter 1 (PAT1). Moreover, the retrograde pathway was mainly involved in the intracellular transport of hybrid micelles and transcytosis delivery. Furthermore, the prominent intestinal mucosa absorption in situ and in vivo liver distribution of the oral hybrid micelle were both detected. The results of this study indicated that the hybrid micelles were capable of conquering the intestinal mucosal barrier, having a great potential for oral application of drugs with poor oral bioavailability.

EGFR-targeted humanized single chain antibody fragment functionalized silica nanoparticles for precision therapy of cancer.

The combination of highly specific targeting ability and potent killing effect has made antibody-drug conjugates (ADCs) a popular area of focus in the development of anti-cancer drugs. However, the large molecular weight of IgG antibodies (∼ 150 kDa) often faces challenges in penetrating capillaries and stroma in tumor tissue. Moreover, when the drug-antibody ratio (DAR) is too low (DAR < 2) or too high (DAR > 6) it decreases the effectiveness of the ADC and further increases the potential for aggregation, overall clearance of the early system payload, and release rate. In this study, an EGFR-based single-chain antibody fragment (husA)-human serum albumin (HSA)-coupled FITC-labeled mesoporous silica nanoparticle (FMSN-DOX-H-husA) was developed. Chinese hamster ovarian cells express the husA, which is a single chain antibody fragment of the EGFR that has been humanized. The small molecular weight of the single chain antibody allows for shorter penetration into solid tumors and the absence of adverse effects of the Fc fragment. The modification of HSA improves the safety of the antibody nanoparticle couples by both improving the biocompatibility of the nanoparticles, prolonging the circulation time of the nanoparticles, and avoiding early release of the payload. Also, the humanization substantially reduces the immunogenicity. More importantly, the ratio of drug antibodies on nanoparticles was experimentally and computationally derived to be 11.8, providing a more accurate guide for clinical trials. The results of both in vivo and in vitro experiments indicated promising antitumor activity and safety of FMSN-DOX-H-husA. Thus, this antibody-drug conjugate provided a hopeful option for cancer treatment.

Molecular genetics and quantitative traits divergence among populations of Eothenomys miletus from Hengduan Mountain region.

An important objective of evolutionary biology has always been to grasp the evolutionary and genetic processes that contribute to speciation. The present work provides the first detailed account of the genetic and physiological adaptation to changing environmental temperatures as well as the reasons causing intraspecific divergence in the Eothenomys miletus from the Hengduan Mountain (HM) region, one of the biodiversity hotspots. One hundred sixty-one E. miletus individuals from five populations in the HM region had their reduced-representation genome sequenced, and one additional individual from each community had their genomes resequenced. We then characterized the genetic diversity and population structure of each population and compared the phenotypic divergence in traits using neutral molecular markers. We detected significant phenotypic and genetic alterations in E. miletus from the HM region that were related to naturally occurring diverse habitats by combining morphometrics and genomic techniques. There was asymmetric gene flow among the E. miletus populations, indicating that five E. miletus populations exhibit an isolation-by-island model, and this was supported by the correlation between F ST and geographic distance. Finally, P ST estimated by phenotypic measures of most wild traits were higher than differentiation at neutral molecular markers, indicating directional natural selection favoring different phenotypes in different populations must have been involved to achieve this much differentiation. Our findings give information on the demographic history of E. miletus, new insights into their evolution and adaptability, and literature for studies of a similar nature on other wild small mammals from the HM region.

Molecular modeling strategy for detailing the primary mechanism of action of copanlisib to PI3K: combined ligand-based and target-based approach.

Since dysregulation of the phosphatidylinositol 3-kinase (PI3K) signaling pathway is associated with the pathogenesis of cancer, inflammation, and autoimmunity, PI3K has emerged as an attractive target for drug development. Although copanlisib is the first pan-PI3K inhibitor to be approved for clinical use, the precise mechanism by which it acts on PI3K has not been fully elucidated. To reveal the binding mechanisms and structure-activity relationship between PI3K and copanlisib, a comprehensive modeling approach that combines 3D-quantitative structure-activity relationship (3D-QSAR), pharmacophore model, and molecular dynamics (MD) simulation was utilized. Initially, the structure-activity relationship of copanlisib and its derivatives were explored by constructing a 3D-QSAR. Then, the key chemical characteristics were identified by building common feature pharmacophore models. Finally, MD simulations were performed to elucidate the important interactions between copanlisib and different PI3K subtypes, and highlight the key residues for tight-binding inhibitors. The present study uncovered the principal mechanism of copanlisib's action on PI3K at the theoretical level, and these findings might provide guidance for the rational design of pan-PI3K inhibitors.Communicated by Ramaswamy H. Sarma.

Developing new PI3Kγ inhibitors by combining pharmacophore modeling, molecular dynamic simulation, molecular docking, fragment-based drug design, and virtual screening.

Since dysregulation of the phosphatidylinositol 3-kinase gamma (PI3Kγ) signaling pathway is associated with the pathogenesis of cancer, inflammation, and autoimmunity, PI3Kγ has emerged as an attractive target for drug development. IPI-549 is the only selective PI3Kγ inhibitor that has advanced to clinical trials, thus, IPI-549 could serve as a promising template for designing novel PI3Kγ inhibitors. In this present study, a modeling strategy consisting of common feature pharmacophore modeling, receptor-ligand pharmacophore modeling, and molecular dynamics simulation was utilized to identify the key pharmacodynamic characteristic elements of the target compound and the key residue information of the PI3Kγ interaction with the inhibitors. Then, 10 molecules were designed based on the structure-activity relationships, and some of them exhibited satisfactory predicted binding affinities to PI3Kγ. Finally, a hierarchical multistage virtual screening method, involving the developed common feature and receptor-ligand pharmacophore model and molecular docking, was constructed for screening the potential PI3Kγ inhibitors. Overall, we hope these findings would provide some guidance for the development of novel PI3Kγ inhibitors.

Transcriptome profiling of genes regulated by phosphate-solubilizing bacteria Bacillus megaterium P68 in potato (Solanum tuberosum L.).

The insoluble phosphorus in the soil is extremely difficult to be absorbed and used directly through the potato root system. Although many studies have reported that phosphorus-solubilizing bacteria (PSB) can promote plant growth and uptake of phosphorus, the molecular mechanism of phosphorus uptake and growth by PSB has not been investigated yet. In the present study, PSB were isolated from rhizosphere soil in soybean. The data of potato yield and quality revealed that the strain P68 was the most effective In the present study, PSB identification, potato field experiment, pot experiment and transcriptome profiling to explored the role of PSB on potato growth and related molecular mechanisms. The results showed that the P68 strain (P68) was identified as Bacillus megaterium by sequencing, with a P-solubilizing ability of 461.86 mg·L-1 after 7-day incubation in National Botanical Research Institute's Phosphate (NBRIP) medium. Compared with the control group (CK), P68 significantly increased the yield of potato commercial tubers by 17.02% and P accumulation by 27.31% in the field. Similarly, pot trials showed that the application of P68 significantly increased the biomass, total phosphorus content of the potato plants, and available phosphorus of the soil up by 32.33, 37.50, and 29.15%, respectively. Furthermore, the transcriptome profiling results of the pot potato roots revealed that the total number of bases was about 6G, and Q30 (%) was 92.35-94.8%. Compared with the CK, there were a total of 784 differential genes (DEGs) regulated when treated with P68, which 439 genes were upregulated and 345 genes were downregulated. Interestingly, most of the DEGs were mainly related to cellular carbohydrate metabolic process, photosynthesis, and cellular carbohydrate biosynthesis process. According to the KEGG pathway analysis, a total of 46 categorical metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were annotated to 101 DEGs found in potato roots. Compared with the CK, most of the DEGs were mainly enriched in glyoxylate and dicarboxylate metabolism (sot00630), nitrogen metabolism (sot00910), tryptophan metabolism (sot00380), and plant hormone signal transduction (sot04075), and these DEGs might be involved in the interactions between Bacillus megaterium P68 and potato growth. The qRT-PCR analysis of differentially expressed genes showed that inoculated treatments P68 significantly upregulated expression of the phosphate transport, nitrate transport, glutamine synthesis, and abscisic acid regulatory pathways, respectively, and the data from qRT-PCR were consistent with that obtained from RNA-seq. In summary, PSB may be involved in the regulation of nitrogen and phosphorus nutrition, glutaminase synthesis, and abscisic acid-related metabolic pathways. This research would provide a new perspective for studying the molecular mechanism of potato growth promotion by PSB in the level of gene expression and related metabolic pathways in potato roots under the application of Bacillus megaterium P68.

Metal-Organic Frameworks Facilitate Nucleic Acids for Multimode Synergistic Therapy of Breast Cancer.

Compared with traditional medical methods, gene therapy and photodynamic therapy are the new fields of cancer treatment, and they more accurately and effectively obtain preferable therapeutic effects. In this study, a chemotherapy drug-free nanotherapeutic system based on ZIF-90 encapsulated with Ce6-G3139 and Ce6-DNAzyme for gene and photodynamic therapies was constructed. Once entering the cancer cell, the therapy system will decompose and release Zn2+, Ce6-G3139, and Ce6-DNAzyme in the acidic environment. On the one hand, G3139 binds to the antiapoptotic gene BCL-2 in tumor cells and downregulates related proteins to inhibit tumor proliferation. On the other hand, Zn2+ produced by the decomposition of ZIF-90 can be used as a cofactor to activate the cleavage activity of DNAzyme to initiate gene therapy. Proliferation and metastasis of tumors were further inhibited by DNAzyme, targeting and cutting the gene of human early growth factor-1 (EGR-1). In addition, the photosensitizer Ce6 carried by the nucleic acid will produce cytotoxic ROS to kill cancer cells after irradiation. The results of this study demonstrated that the designed nanoplatform, which synergistically combines gene and photodynamic therapies, has shown great potential for cancer treatment.

Constructed Tumor-Targeted and MMP-2 Biocleavable Antibody Conjugated Silica Nanoparticles for Efficient Cancer Therapy.

Antibody-drug conjugates (ADC) are an inevitable trend in the development of modern "precision medicine". The goal of this work is to produce enzyme-responsive antibody nanoparticle-loaded medication (FMSN-Dox-H2-AE01) based on the EGFR antibody (AE01) and human serum albumin (HSA) shelled mesoporous silica nanoparticles. HSA and antibodies on the surface of the particlescan not only enhance the biocompatibility of the particle and avoid early drug leakage but also allow selective biodegradation triggered by matrix metalloproteinase-2 (MMP-2), which are overexpressed enzymes in some tumor tissues. The cytotoxicity test confirmed favorable safety and efficacy of the ADC. The mortality rate of cancer cells is about 85-90%. Moreover, the antibody nanoparticle-loaded drug showed distinguishing controlled release efficiency toward cancer cells induced by different levels of MMP-2 and pH. This enzyme-responsive FMSN-Dox-H2-AE01 offers a promising option for cancer therapy.

Analysis of the in vitro function and internalization ability of a humanized EGFR antibody AE01 expressed by Chinese hamster ovary cells.

The primary objective of this study was to obtain humanized EGFR antibody and to study it in vitro binding and endocytosis to A431 epidermoid carcinoma cells overexpressing EGFR. Firstly, humanized anti-EGFR AE01 was stably expressed in CHO system. The expression of AE01 was detected by SDS-PAGE and Western blot. The binding and endocytosis of AE01 were detected by flow cytometry and immunofluorescence assay. The results showed that: (1) Pure humanized AE01 was prepared, (2) AE01 specifically binds to A431 cells on the cell surface (EGFR-positive), but not binds to NIH 3T3 cells (EGFR-negative), (3) AE01 can effectively inhibit the proliferation of A431 cells, and (4) AE01 binds to A431 cell surface triggered internalization. The antibody is expected to be a candidate molecule for EGFR overexpressed cancer cell targeted therapeutic vectors.

A comprehensive evaluation of stable expression "hot spot" in the ScltI gene of Chinese hamster ovary cells.

The Chinese hamster ovary (CHO) cell is the most widely used biopharmaceutical expression system, but its long-term expression is unstable. This issue can be effectively addressed by site-specific integration of exogenous genes into the genome. Therefore, exogenous protein sites with stable expression in the CHO cell genome must be identified. CRISPR/Cas9 technology was used in this study to integrate various exogenous genes into the ScltI site as a "hot spot" at the CHO-K1 cell genome NW_003614095.1, and the stability and adaptability of exogenous genes expressed at the site were investigated. Flow cytometry sorting technology was used to obtain positive monoclonal cell lines that expressed either intracellular protein green fluorescent protein (EGFP) or secretory protein human serum albumin (HSA). For 60 passages, the positive monoclonal cell lines' cell growth cycles and exogenous protein expression were both observed. The results demonstrated that integrating the gene encoding exogenous proteins into the ScltI site had no effect on cell growth. The fluorescence intensity of EGFP was similar after 60 passages, and the expression of HSA increased slightly. Additionally, the super-monomeric protein VWF hydrolase (ADAMTS13) (190 kDa), human coagulation factor VII (FVII) (55 kDa), and interferon α2b (12 kDa) were integrated into the ScltI site for expression. In conclusion, the site located in the first exon of the ScltI gene within the CHO-K1 cell genome NW_003614095.1 is an ideal "hot spot" for the stable expression of various exogenous proteins. KEY POINTS: • The site-specific integration strategy of an exogenous gene in CHO cells was established for the ScltI site. • The genes for EGFP and HSA were site-directed integrated and stably expressed at the ScltI site. • The ScltI site fulfills the expression of exogenous proteins of different molecular weight sizes (15-190 kDa).

Hypoxia-responsive covalent organic framework by single NIR laser-triggered for multimodal synergistic therapy of triple-negative breast cancer.

In recent years, laser-mediated photodynamic therapy and photothermal therapy have attracted widespread attention due to their minimally invasive, easy to operate characteristics and high specificity. However, the traditional photodynamic or photothermal therapy exist several shortcomings such as the hypoxic microenvironment, intracellular heat shock proteins or complex operation. In this study, covalent organic framework (COF) was used as the drug carrier to equip with the photosensitizer indocyanine green (ICG) and the hypoxia-activating prodrug AQ4N. The hyaluronic acid (HA) was modified on the surface of COF to obtain the HA-COF@ICG/AQ4N drug delivery system. HA-modified COF delivery systems can target tumor cells through recognize CD44 which is overexpressed in the surface of tumor cells membrane. Under the irradiation of single NIR laser, ICG that can excite the nanoplatform simultaneously produces a combined effect of photodynamic and photothermal. At the same time, photodynamic therapy through depleting intracellular oxygen exacerbates the hypoxic state of the tumor microenvironment, which in turn enhances AQ4N reduced to chemotherapeutic drug AQ4, producing a synergistic cascade antitumor effect. The results of our study by tumor cell and tumor spheroids indicated that the hypoxia-activated multi-functional nanoplatform could effectively inhibit the growth and metastasis of triple-negative breast cancer.

Developing a Naïve Bayesian Classification Model with PI3Kγ structural features for virtual screening against PI3Kγ: Combining molecular docking and pharmacophore based on multiple PI3Kγ conformations.

Phosphatidylinositol 3-kinase gamma (PI3Kγ) plays a critical role in immune signaling, thus identifying PI3Kγ as a potential therapeutic target. However, developing selective PI3Kγ inhibitors is hampered by the highly conserved structure of the ATP-binding pocket. Focused effort would be needed to improve upon the γ-subtype selectivity of the inhibitors; therefore, in the present study, a naïve Bayesian classification (NBC) model with PI3Kγ structural features that integrates molecular docking and pharmacophore based on multiple PI3Kγ conformations was developed for virtual screening against PI3Kγ to find novel selective PI3Kγ inhibitors. First, the active PI3Kγ inhibitors/decoy dataset was used to prove whether molecular docking or pharmacophore, integrating multiple PI3Kγ conformations always has higher prediction accuracy than that of any single conformation. Second, both internal cross-validation and external prediction revealed that the NBC model combining molecular docking and pharmacophore could significantly improve the enrichment of active PI3Kγ inhibitors. Then, an analog dataset based on JN-PK1 (a reference compound) was constructed and submitted to virtual screening using the optimal NBC model. Finally, a novel inhibitor with higher PI3Kγ inhibitory activity than JN-PK1 was identified through a series of biological assays, showing both good accuracy and significant reliability of the NBC model with the PI3Kγ structural features. We hope that the developed virtual screening strategy will provide valuable guidance for the discovery of novel selective PI3Kγ inhibitors.