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Some microbial volatile organic compounds (mVOCs) can act as antagonistic weapons against plant pathogens, but little information is available on the contribution of individual mVOC to biocontrol and how they interact with plant pathogens. In this study, the Bacillus subtilis strain N‐18 isolated from the rhizosphere of healthy plants grown in areas where Fusarium crown and root rot (FCRR) of tomato occurs could reduce the 30% of the incidence of FCRR. Moreover, the volatile organic compounds (VOCs) produced by N‐18 had inhibitory effects on Fusarium oxysporum f. sp. radicis‐lycopersici (FORL). The identification of VOCs of N‐18 was analyzed by the solid‐phase microextraction coupled to gas chromatography‐mass spectrometry. Meanwhile, we conducted sensitivity tests with these potential active ingredients and found that the volatile substances acetoin and 2‐heptanol can reduce the 41.33% and 35% of the incidence of FCRR in tomato plants. In addition, the potential target protein of acetoin, found in the cheminformatics and bioinformatics database, was F. oxysporum of hypothetical protein AU210_012600 (FUSOX). Molecular docking results further predicted that acetoin interacts with FUSOX protein. These results reveal the VOCs of N‐18 and their active ingredients in response to FORL and provide a basis for further research on regulating and controlling FCRR. [ABSTRACT FROM AUTHOR]

Ralstonia solanacearum usually infects the vascular bundle system through the roots of host plants, causing bacterial wilt and leading to irreversible wilting and death of plants. Bacterial wilt is a devastating soil-borne bacterial disease. At present, it has been one of the main diseases restricting the production of Solanaceae crops in China. Type Ⅲ secretion system (T3SS) plays an important role in the pathogenesis of R. solanacearum, using T3SS to inject large amounts of Type Ⅲ effectors (T3Es) into host cells to interfere with the immune response of the host. Scholars at home and abroad are committed to exploring how R. solanacearum interferes with host cells and regulates host immune function by identifying target proteins in the host. Therefore, the identification of host proteins that can be targeted by T3Es is helpful to understand the biological function of R. solanacearum T3Es, the pathogenic process of R. solanacearum, and to explore the R. solanacearum resistance-related proteins and their mechanism of action in hosts. Although most of the functions of T3Es are still unknown, so far, it has been reported that R. solanacearum T3Es can regulate host resistance to bacterial wilt by interfering with plant innate immunity, inducing plant hypersensitivity response and affecting plant metabolism and hormone signal transduction through a variety of molecular mechanisms. In this review, we summarize the current research progress on the characteristics and functional identification methods of T3Es of R. solanacearum, and its research progress in participating in the regulation of pathogenicity and plant immunity mechanism of R. solanacearum, which can provide an in-depth understanding of the pathogenic mechanism of R. solanacearum and the response mechanism of the host immune system. The mechanism of interaction between R. solanacearum T3Es and the host are prospected, which will provide an effective reference for the analysis of the host resistance mechanism induced by R. solanacearum and the prevention and control of bacterial wilt.

Ralstonia solanacearum usually infects the vascular bundle system through the roots of host plants, causing bacterial wilt and leading to irreversible wilting and death of plants. Bacterial wilt is a devastating soil-borne bacterial disease. At present, it has been one of the main diseases restricting the production of Solanaceae crops in China. Type Ⅲ secretion system (T3SS) plays an important role in the pathogenesis of R. solanacearum, using T3SS to inject large amounts of Type Ⅲ effectors (T3Es) into host cells to interfere with the immune response of the host. Scholars at home and abroad are committed to exploring how R. solanacearum interferes with host cells and regulates host immune function by identifying target proteins in the host. Therefore, the identification of host proteins that can be targeted by T3Es is helpful to understand the biological function of R. solanacearum T3Es, the pathogenic process of R. solanacearum, and to explore the R. solanacearum resistancerelated proteins and their mechanism of action in hosts. Although most of the functions of T3Es are still unknown, so far, it has been reported that R. solanacearum T3Es can regulate host resistance to bacterial wilt by interfering with plant innate immunity, inducing plant hypersensitivity response and affecting plant metabolism and hormone signal transduction through a variety of molecular mechanisms. In this review, we summarize the current research progress on the characteristics and functional identification methods of T3Es of R. solanacearum, and its research progress in participating in the regulation of pathogenicity and plant immunity mechanism of R. solanacearum, which can provide an in-depth understanding of the pathogenic mechanism of R. solanacearum and the response mechanism of the host immune system. The mechanism of interaction between R. solanacearum T3Es and the host are prospected, which will provide an effective reference for the analysis of the host resistance mechanism induced by R. solanacearum and the prevention and control of bacterial wilt. [ABSTRACT FROM AUTHOR]

Keloid is characterized as the fibrotic tissue resulting from the increase of fibroblast activity. Uncaria gambir (Hunter) Roxb. possesses bioactive compounds that have potential as antifibrotic agents, while the mechanism of action in keloid has not yet been elucidated. The aim of this study was to investigate the interaction of gambir bioactive compounds with keloid target proteins using an epistatic and molecular simulation approach. The known bioactive compounds of gambir targets and keloid-related protein targets were screened using databases. The network was constructed and analyzed to obtain the core protein targets. The targets were enriched to describe the Gene Ontology (GO) and pathway related to the proteins. Eleven targets were defined as the main targets of gambir bioactive compounds related to keloid disease. Gambiriin C, Isogambirine, and Procyanidin B1 were identified as the most promising compounds with the highest binding energy to transforming growth factor beta 1 (TGFβ1), AKT serine/threonine kinase 1 (AKT1), and matrix metallopeptidase 1 (MMP1) as the target proteins. GO enrichment and pathway analysis found that gambir bioactive compounds may act on keloid-related target proteins to regulate cell proliferation, migration, transcription, and signal transduction activity via profibrotic cytokine and growth factor signaling pathways. This study provides a reference for potential targets, compounds, and pathways to explain the mechanism of gambir against keloid. [ABSTRACT FROM AUTHOR]

Introduction: The Hail Desert Plant Database serves as an extensive repository that has been created to consolidate and systematize information concerning medicinal plants that are native to the arid Hail region in Saudi Arabia. Materials and Methods: By conducting thorough literature mining from credible sources such as scientific articles and online databases, we systematically collected and organized data on more than 200 desert plant species. This comprehensive dataset includes botanical characteristics, phytochemical compositions, traditional applications, habitat preferences, documented medicinal uses, and the active compounds associated with these plants. In addition, we utilized molecular docking methodologies to perform computational investigations that aimed to elucidate the molecular interactions occurring between phytochemical compounds and target proteins that are known to be associated with the specific diseases traditionally treated by these plants. Results: The database, which has been meticulously crafted to feature a user-friendly interface, offers an indispensable resource for researchers and clinicians who are captivated by the therapeutic possibilities presented by these arid florae. The inclusion of three-dimensional structures of docked complexes in the database significantly enhances its research capabilities, enabling comprehensive investigations and assisting in the development of potential drug candidates derived from natural sources. Conclusion: The Hail Desert Plant Database serves as a crucial tool, facilitating progress in the field of drug discovery, investigations into structural biology, and the examination of alternative therapeutic agents derived from the diverse array of desert plants. The Hail Desert Plant Database is freely accessible at http://haildesertplants.com/. [ABSTRACT FROM AUTHOR]

Cucurbitacins have high economic value as they are a major source of food and have pharmacological properties. Cucurbitacin I (CuI) is a plant‐derived natural tetracyclic triterpenoid compound that shows an anticancer effect via inhibiting the JAK2‐STAT3 signaling pathway. The actin cytoskeleton is the most abundant protein in cells and regulates critical events through reorganization in cells. In this study, it is aimed at determining the direct effect of CuI on actin dynamics. The fluorescence profile of G‐actin in the presence of CuI (1–200 nM) shifted to a higher temperature, suggesting that G‐actin binds CuI and that G‐actin–CuI is more thermally stable than the ligand‐free form. CuI dose‐dependently inhibited the polymerization of F‐actin in vitro and disrupted actin filaments in endothelial cells. Docking and MD simulations suggested that CuI binds to the binding site formed by residues I136, I175, D154, and A138 that are at the interface of monomers in F‐actin. The migration ability of cells treated with CuI for 24 h was significantly lower than the control group (p <.001). This study reveals the molecular mechanisms of CuI in the regulation of actin dynamics by binding G‐actin. More importantly, this study indicates a novel role of CuI as an actin‐targeting drug by binding directly to G‐actin and may contribute to the mode of action of CuI on anticancer activities. [ABSTRACT FROM AUTHOR]

Introduction: Carnosol exhibited ameliorating effects on muscle atrophy of mice developed cancer cachexia in our previous research. Method: Here, the ameliorating effects of carnosol on the C2C12 myotube atrophy result from simulated cancer cachexia injury, the conditioned medium of the C26 tumor cells or the LLC tumor cells, were observed. To clarify the mechanisms of carnosol, the possible direct target proteins of carnosol were searched using DARTS (drug affinity responsive target stability) assay and then confirmed using CETSA (cellular thermal shift assay). Furthermore, proteomic analysis was used to search its possible indirect target proteins by comparing the protein expression profiles of C2C12 myotubes under treatment of C26 medium, with or without the presence of carnosol. The signal network between the direct and indirect target proteins of carnosol was then constructed. Results: Our results showed that, Delta-1-pyrroline-5-carboxylate synthase (P5CS) might be the direct target protein of carnosol in myotubes. The influence of carnosol on amino acid metabolism downstream of P5CS was confirmed. Carnosol could upregulate the expression of proteins related to glutathione metabolism, anti-oxidant system, and heat shock response. Knockdown of P5CS could also ameliorate myotube atrophy and further enhance the ameliorating effects of carnosol. Discussion: These results suggested that carnosol might ameliorate cancer cachexia-associated myotube atrophy by targeting P5CS and its downstream pathways. [ABSTRACT FROM AUTHOR]

Programmed death ligand-1 (PD-L1) is highly expressed in a variety of cancer cells and suggests a poorer prognosis for patients. The natural compound isorhamnetin (ISO) shows promise in treating cancers and causing damage to canine mammary tumor (CMT) cells. We investigated the mechanism of ISO in reducing PD-L1 expression in CMT cells. Clustered, regularly interspaced short palindromic repeat-associated protein 9 (CRISPR/Cas9) was used to mediate CD274 knockout in U27 cells. Then, monoclonal cells were screened and cultured. Nucleotide sequencing and expression of PD-L1 were detected. Additionally, we examined cell migration, invasion, and damage. Immunofluorescent staining of PD-L1 was examined in U27 cells. The signaling pathways were measured by Western blotting. Murine xenotransplantation models and murine immunocompetent allograft mammary tumor models were established to evaluate the effect of ISO therapy. Expression of Ki-67, caspase3, and PD-L1 were analyzed by immunohistochemistry. A pull-down assay was used to explore which proteins could bind to ISO. Canine EGFR protein was purified and used to detect whether it directly binds to ISO using a surface plasmon resonance assay. ISO inhibited the EGFR-STAT3-PD-L1 signaling pathway and blocked cancer growth, significantly increasing the survival rate of healthy cells. The cell membrane receptor EGFR was identified as a direct target of ISO. ISO could be exploited as an antineoplastic treatment of CMT by targeting EGFR to suppress PD-L1 expression. [ABSTRACT FROM AUTHOR]

Abstract Background Prostate cancer is a disease that seriously troubles men. However, there are some inevitable limitations in interventional therapy for prostate cancer patients at present, most of which are caused by low selectivity and high toxic side effects due to unclear drug targets. In this study, we identified the target protein of Curcusone C with anti-prostate cancer potential activity and verified its target and mechanism of action. Methods Click chemistry-activity based proteomics profiling (CC-ABPP) method was used to find target protein of Curcusone C against prostate cancer. Competitive CC-ABPP, drug affinity responsive target stability (DARTS) and surface plasmon resonance (SPR) methods were used to verifying the target protein. Moreover, potential mechanism was validated by western blot in vitro and by hematoxylin-eosin (HE) staining, detection of apoptosis in tumor tissue (TUNEL), and immunohistochemical (IHC) in vivo. Results We found that poly(rC)-binding protein 2 (PCBP2) was the target protein of Curcusone C. In addition, Curcusone C might disrupt the Bax/Bcl-2 balance in PC-3 cells by inhibiting the expression of the target protein PCBP2, thereby inducing mitochondrial damage and activation of the mitochondrial apoptosis pathway, and ultimately inducing apoptosis of prostate cancer cells. Conclusions Curcusone C is a potential compound with anti-prostate cancer activity, and this effect occurs by targeting the PCBP2 protein, which in turn may affect the TGF/Smad signaling pathway and Bax/Bcl-2 balance. Our results laid a material and theoretical foundation for Curcusone C, to be widely used in anti-prostate cancer.

Background: Prostate cancer is a disease that seriously troubles men. However, there are some inevitable limitations in interventional therapy for prostate cancer patients at present, most of which are caused by low selectivity and high toxic side effects due to unclear drug targets. In this study, we identified the target protein of Curcusone C with anti-prostate cancer potential activity and verified its target and mechanism of action. Methods: Click chemistry-activity based proteomics profiling (CC-ABPP) method was used to find target protein of Curcusone C against prostate cancer. Competitive CC-ABPP, drug affinity responsive target stability (DARTS) and surface plasmon resonance (SPR) methods were used to verifying the target protein. Moreover, potential mechanism was validated by western blot in vitro and by hematoxylin-eosin (HE) staining, detection of apoptosis in tumor tissue (TUNEL), and immunohistochemical (IHC) in vivo. Results: We found that poly(rC)-binding protein 2 (PCBP2) was the target protein of Curcusone C. In addition, Curcusone C might disrupt the Bax/Bcl-2 balance in PC-3 cells by inhibiting the expression of the target protein PCBP2, thereby inducing mitochondrial damage and activation of the mitochondrial apoptosis pathway, and ultimately inducing apoptosis of prostate cancer cells. Conclusions: Curcusone C is a potential compound with anti-prostate cancer activity, and this effect occurs by targeting the PCBP2 protein, which in turn may affect the TGF/Smad signaling pathway and Bax/Bcl-2 balance. Our results laid a material and theoretical foundation for Curcusone C, to be widely used in anti-prostate cancer. [ABSTRACT FROM AUTHOR]

Background: Advances in genomics and taxonomic literature reveal that lung cancer is a polygenic disease and expose the complexity of cancer-related genes and molecular mechanisms. Several chemically synthesized drugs are used in cancer treatment, but this is still a challenging task because of their lower efficacy and side effects. In recent years, phytochemicals have played a vital role in novel drug discovery; garlic was used in this study to treat lung cancer. This study aimed to determine the specific target, pharmacological, and molecular mechanisms of garlic phytoconstituents in lung cancer treatment. Methodology: Protein-protein interaction network and KEGG signaling pathway analysis of no small cell lung cancer and garlic phytoconstituents revealed that out of 68 targets of non-small cell lung cancer, 14 were targeted by garlic phytoconstituents. Results: Only 14 phytoconstituents of Allium sativum L. have regulatory effects on 14 targets of non-small cell lung cancer. Garlic phytoconstituents have an inhibitory effect on lung cancer progression by regulating highly enriched pathways in lung cancer, such as the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor resistance pathway. Conclusion: Some garlic phytoconstituents, such as allixin, ajoene, carvacrol, and some derivative of allicin have drug-like properties that target these targets and act by regulating different molecular pathways of cancer progression. The results of this study require further in vivo or experimental studies to confirm their value in lung cancer treatment and to identify the exact binding sites of the selected targets on which ligands can bind. [ABSTRACT FROM AUTHOR]

Keloid is characterized as the fibrotic tissue resulting from the increase of fibroblast activity. Uncaria gambir (Hunter) Roxb. possesses bioactive compounds that have potential as antifibrotic agents, while the mechanism of action in keloid has not yet been elucidated. The aim of this study was to investigate the interaction of gambir bioactive compounds with keloid target proteins using an epistatic and molecular simulation approach. The known bioactive compounds of gambir targets and keloid-related protein targets were screened using databases. The network was constructed and analyzed to obtain the core protein targets. The targets were enriched to describe the Gene Ontology (GO) and pathway related to the proteins. Eleven targets were defined as the main targets of gambir bioactive compounds related to keloid disease. Gambiriin C, Isogambirine, and Procyanidin B1 were identified as the most promising compounds with the highest binding energy to transforming growth factor beta 1 (TGFβ1), AKT serine/threonine kinase 1 (AKT1), and matrix metallopeptidase 1 (MMP1) as the target proteins. GO enrichment and pathway analysis found that gambir bioactive compounds may act on keloid-related target proteins to regulate cell proliferation, migration, transcription, and signal transduction activity via profibrotic cytokine and growth factor signaling pathways. This study provides a reference for potential targets, compounds, and pathways to explain the mechanism of gambir against keloid.

Pyridazinone derivatives have been extensively used as anticancer agents. IMB5036 is a structure specific pyridazinone compound with potential antitumor activity via targeting KSRP protein which controls gene expression at multiple levels. In this study, fifteen IMB5036 analogues were synthesized and preliminary structure-activity relationships were explored. Among them, compounds 8 and 10 exhibited remarkably anti-proliferation of various cancer cells and a good cancer cell selectivity (against human fetal hepatocyte L02 cells). More detailed investigation was included that both 8 and 10 inhibited colony formation and migration in concentration-dependent mode against MCF-7 cells. Additionally, 8 and 10 induced apoptosis and cell cycle arrest, decreased mitochondrial membrane potential, damaged DNA, and increased reactive oxygen species. Moreover, 8 displayed a potent antitumor efficacy (TGI = 74.2 %, at a dose of 30 mg/kg) in MCF-7 xenograft model by i.p. injection. Further, we synthesized a biotinylated probe 16 for identifying the detail domain of KSRP. Through pull down assay and molecular docking study, we validated that the KH23 domain functioned as the binding pocket for the compounds. Thus, compound 8 was identified as a novel targeting KSRP pyridazinone-based compound and exhibited excellent antitumor activity both in vitro and in vivo. [Display omitted] • Fifteen IMB5036 derivatives were synthesized and investigated as antitumor agents. • Compounds 8 and 10 displayed potent cytotoxicity in multiple cancer cells. • Compound 8 showed binding affinity to KSRP, especially binding to KH23 domain. • Compound 8 had potent in vivo antitumor effects. [ABSTRACT FROM AUTHOR]

Swertia Mussotti is used as febrifuge, analgesic and to treat calculous cholecystitis, however, the underling mechanism remains unclear. This study investigates the therapeutic effect of the active fraction named iridoid and xanthone glycoside (IXG) extracted from S. mussotii on six animal models related to calculous cholecystitis and its complications, and to explore its potential target proteins. Four main compounds including swertiamarin (STR), sweroside (SRS), gentiopicroside (GPS) and mangiferin (MGR) were identified from the IXG by UHPLC-TOF-MS. The in vivo experiments results confirmed that IXG significantly decreased the level of total bilirubin (TBIL), direct bilirubin (DBIL) and cyclooxygenase-2 (COX2) in calculous cholecystitis. IXG treatment dramatically reduced the number of twists and the time of clicking foot in 2nd phase induced by glacial acetic acid and formalin, however, no effect was showed on central pain established by hot plate test. IXG also significantly decreased the anal temperature induced by yeast and 2,4-dinitrophenol. These results indicated that IXG alleviate calculous cholecystitis and its clinical symptom. In addition, IXG suppressed the expression of Prostaglandin E2 (PGE2) in vitro. Mechanistically, COX2 was identified as the direct target of IXG in RAW264.7 cells, and downregulated the protein levels of COX2. The results confirmed that IXG ameliorates calculous cholecystitis and its clinical symptom (pain and fever) by suppressing the production of PGE2 through targeting COX2. [Display omitted] • IXG protects against the liver injury induced by calculous cholecystitis. • IXG inhibits peripheral pain induced by glacial acetic acid and formalin, respectively. • IXG inhibits inflammatory fever induced by yeast and non-inflammatory fever induced by 2,4-dinitrophenol. • IXG exerts analgesia and antipyretic effect by targeting COX2 to reduce the production of PGE2 in vitro. [ABSTRACT FROM AUTHOR]

BackgroundThe most aggressive subtype of breast cancer, triple-negative breast cancer (TNBC), has a worse prognosis and a higher probability of relapse since there is a narrow range of treatment options. Identifying and testing potential therapeutic targets for the treatment of TNBC is of high priority.MethodsUsing a transcriptional signature of triple-negative breast cancer collected from Gene Expression Omnibus (GEO), CMap was utilized to reposition compounds for the treatment of TNBC. CCK8 and colony formation experiments were performed to detect the effect of the candidate drug on the proliferation of TNBC cells. Meanwhile, transwell and wound healing assay were implemented to detect cell metastasis change caused by the candidate drug. Moreover, the proteomic approach was presently ongoing to evaluate the underlying mechanism of the candidate drug in TNBC. Furthermore, drug affinity responsive target stability (DARTS) coupled with LC-MS/MS was carried out to explore the potential drug target candidate in TNBC cells.ResultsWe found that the most widely used medication, eugenol, reduced the growth and metastasis of TNBC cells. According to the underlying mechanism revealed by proteomics, eugenol could inhibit TNBC cell proliferation and metastasis via the NOD1-NF-κB signaling pathway. DARTS experiment further revealed that eugenol may bind to NF-κB in TNBC cells.ConcludesOur findings pointed out that eugenol was a potential candidate drug for the treatment of TNBC.

BACKGROUND: Due to low price, safety and effectiveness, anti caries DNA vaccine is expected to become an important means of human anti caries. Scholars are looking for an effective immune pathway to induce antibody production or a sustained-release system and adjuvant to protect vaccine titer, which has become a research focus in recent years. OBJECTIVE: To observe the immune effect of the sustained release hydrogel poly(lactic/glycolic acid)-polyethylene glycol-poly(lactic/glycolic acid) loaded with anti-caries gene vaccine pVAX1-SpaP/P. METHODS: The recombinant plasmid pVAX1-SpaP/P and the empty plasmid pVAX1 were loaded with poly(lactic/glycolic acid)-polyethylene glycol-poly(lactic/ glycolic acid) hydrogel, respectively. Twenty-eight New Zealand white rabbits were randomly divided into seven groups. Quadriceps femoris injection, submandibular gland subcutaneous injection, oral administration, and nasal drip injection of hydrogel loaded with recombinant plasmid pVAX1-SpaP/P were performed in four groups. The remaining groups were the control groups. In the negative control group 1, quadriceps muscle was injected with hydrogel loaded with empty plasmid pVAX1. In the negative control group 2, hydrogel loaded with empty plasmid pVAX1 was orally taken. The quadriceps femoris of the blank control group was injected with saline. The immunization was enhanced once a week after the initial immunization. The second immunization was conducted one week apart, and immunized for the third time after an interval of two weeks. ELISA was used to detect anti-SpaP IgA antibody in saliva and anti-SpaP IgG antibody in serum before and after immunization. At 3 days after the end of the three immunizations, the expression of pVAX1-SpaP/P protein was observed by immunohistochemistry technique. RESULTS AND CONCLUSION: (1) Two weeks after immunization with hydrogels loaded with recombinant plasmid pVAX1-SpaP/P via different pathways, the levels of anti-SpaP IgA antibody in saliva and anti-SpaP IgG antibody in serum were significantly increased in rabbits. Anti-SpaP IgG antibody level reached a peak at 10 weeks; anti-SpaP IgA antibody level reached a peak at 6 weeks. Anti-SpaP IgG antibody levels in the oral group were higher than those in the other six groups at 6-12 weeks (P < 0.05). Anti-SpaP IgA antibody levels were higher in the submandibular gland group than those in the other six groups at 4-8 weeks (P < 0.05). (2) One week after immunization with hydrogels loaded with recombinant plasmid pVAX1-SpaP/P via different pathways, anti-SpaP IgA antibody levels increased and peaked at 8 weeks. The antibody levels were higher in the submandibular gland group than those in the other six groups at 1-6 weeks (P < 0.05). The antibody levels were higher in the oral group than those in the other six groups at 8-12 weeks (P < 0.05). Anti-SpaP IgG antibody level in rabbit saliva began to increase at 2 weeks after immunization, and reached a peak at 10 weeks. The antibody levels of the oral group were higher than those in the other six groups at 2, 3, and 6 weeks (P < 0.05). The antibody levels of the quadriceps femoris group at 10 weeks were higher than those of the other six groups (P < 0.05). (3) After immunization with hydrogels loaded with recombinant plasmid pVAX1-SpaP/P via different pathways, immunohistochemical staining showed that positive pVAX1-SpaP/P protein expression in the injection site tissues. (4) The results showed that the poly(lactic/glycolic acid)-polyethylene glycolpoly( lactic/glycolic acid) hydrogel loaded pVAX1-SpaP/P anti caries vaccine could induce specific antibody production in the four ways to induce the immune effect and maintain long time. [ABSTRACT FROM AUTHOR]

Proteolysis-targeting chimera (PROTAC) is a heterobifunctional molecule. Typically, PROTAC consists of two terminals which are the ligand of the protein of interest (POI) and the specific ligand of E3 ubiquitin ligase, respectively, via a suitable linker. PROTAC degradation of the target protein is performed through the ubiquitin–proteasome system (UPS). The general process is that PROTAC binds to the target protein and E3 ligase to form a ternary complex and label the target protein with ubiquitination. The ubiquitinated protein is recognized and degraded by the proteasome in the cell. At present, PROTAC, as a new type of drug, has been developed to degrade a variety of cancer target proteins and other disease target proteins, and has shown good curative effects on a variety of diseases. For example, PROTACs targeting AR, BR, BTK, Tau, IRAK4, and other proteins have shown unprecedented clinical efficacy in cancers, neurodegenerative diseases, inflammations, and other fields. Recently, PROTAC has entered a phase of rapid development, opening a new field for biomedical research and development. This paper reviews the various fields of targeted protein degradation by PROTAC in recent years and summarizes and prospects the hot targets and indications of PROTAC. [ABSTRACT FROM AUTHOR]

Simple Summary: Near-infrared photoimmunotherapy (NIR-PIT) is a novel molecularly-targeted therapy that induces rapid cancer cell death by systemically administering an antibody-photoabsorber conjugate (APC) that binds to cancer cells and irradiating NIR light that drives photochemical transformations of the APC. APCs are constructed by using a monoclonal antibody targeting a cancer cell surface antigen and conjugating it to IRDye700DX silica-phthalocyanine dye. NIR-PIT can selectively kill cancer cells while leaving normal tissues unaffected. Moreover, NIR-PIT activates anti-cancer immunity through the induction of immunogenic cell death of cancer cells. Currently, NIR-PIT is being applied clinically in head and neck squamous cell carcinoma. In previous preclinical studies, NIR-PIT showed excellent efficacy against urologic cancers including bladder cancer and prostate cancer. The clinical application of NIR-PIT will expand to urologic cancers in the near future. Near-infrared photoimmunotherapy (NIR-PIT) is a novel molecularly-targeted therapy that selectively kills cancer cells by systemically injecting an antibody-photoabsorber conjugate (APC) that binds to cancer cells, followed by the application of NIR light that drives photochemical transformations of the APC. APCs are synthesized by selecting a monoclonal antibody that binds to a receptor on a cancer cell and conjugating it to IRDye700DX silica-phthalocyanine dye. Approximately 24 h after APC administration, NIR light is delivered to the tumor, resulting in nearly-immediate necrotic cell death of cancer cells while causing no harm to normal tissues. In addition, NIR-PIT induces a strong immunologic effect, activating anti-cancer immunity that can be further boosted when combined with either immune checkpoint inhibitors or immune suppressive cell-targeted (e.g., regulatory T cells) NIR-PIT. Currently, a global phase III study of NIR-PIT in recurrent head and neck squamous cell carcinoma is ongoing. The first APC and NIR laser systems were approved for clinical use in September 2020 in Japan. In the near future, the clinical applications of NIR-PIT will expand to other cancers, including urologic cancers. In this review, we provide an overview of NIR-PIT and its possible applications in urologic cancers. [ABSTRACT FROM AUTHOR]

Background: The Aim of the present research article is to proposing a conservative approach for the Cassia fistula by using of small branches instead of stem bark because of plant has many important chemical constituents which show different medicinal activity so consumption of plant is high. We studied here Comparative preliminary phytochemical screening test of the ethanol extract and aqueous extract of the stem bark and small branches of Cassia fistula obtained by cold maceration process. Physicochemical analysis of Cassia fistula was done to ascertain the quality of the raw material used in the study. Successive soxhlet extraction method used for the successive extraction of stem bark and small branches with different solvents for comparative chemical profile study by HPLC, LCMS, and GCMS. Molecular Docking Interaction of Abundant Medicinal Phytochemicals in the Liquid Chromatography−Mass Spectrometry (LC−MS) Analysis Data of C. fistula with the L. donovani Drug Target Proteins and Pancreatic lipase colipase target protein. Result: The pH of the small branches was found slightly higher as compared to stem bark and the percentage of other parameters like total ash content, acid insoluble ash, loss on drying at 105 °C, water soluble extractive and alcohol soluble extractive values were found fewer in the small branches as compare to stem bark of the plant. It was observed that the number of peaks in stem bark and small branches of the plant sample were almost similar and the retention time of each peak in stem bark was coincide with the retention of small branches of the sample. Therefore, similarity was observed in stem bark and small branches of the Cassia fistula plant in HPLC, LC-MS and GC-MS. The results obtained from HPLC analysis shows that stem bark contains 0.0084% and small branches having 0.0257% of rhein in Cassia fistula. Compounds 3, 9 and 12 are present in Stem bark as well as small branches of C. fistula and Compounds 22, 32 and 37 are present in small branches only. All the compounds have very good binding energy (Kcal/mol) with the respective target proteins. Conclusion: The small branches have more active chemical constituents than stem bark against particular target proteins.

Simple Summary: Determining the drug–target relationships is the key to modern drug development, and it plays a crucial role in drug side effects research and individual treatment. However, traditional drug target identification by bio-experimental methods is often difficult to develop due to limitations of precision, flux and cost. With the rapid development of bioinformatics and computational biology, the computer-assisted drug–target interaction (DTIs) prediction approach has attracted great attention by researchers as an accurate and quick mean of drug target recognition. In this study, combined with the protein sequence information and drug molecular structure information, a prediction method of DTIs based on machine learning is developed to achieve the purpose of locking targets and saving costs for new drug research. As the basis for screening drug candidates, the identification of drug–target interactions (DTIs) plays a crucial role in the innovative drugs research. However, due to the inherent constraints of small-scale and time-consuming wet experiments, DTI recognition is usually difficult to carry out. In the present study, we developed a computational approach called RoFDT to predict DTIs by combining feature-weighted Rotation Forest (FwRF) with a protein sequence. In particular, we first encode protein sequences as numerical matrices by Position-Specific Score Matrix (PSSM), then extract their features utilize Pseudo Position-Specific Score Matrix (PsePSSM) and combine them with drug structure information-molecular fingerprints and finally feed them into the FwRF classifier and validate the performance of RoFDT on Enzyme, GPCR, Ion Channel and Nuclear Receptor datasets. In the above dataset, RoFDT achieved 91.68%, 84.72%, 88.11% and 78.33% accuracy, respectively. RoFDT shows excellent performance in comparison with support vector machine models and previous superior approaches. Furthermore, 7 of the top 10 DTIs with RoFDT estimate scores were proven by the relevant database. These results demonstrate that RoFDT can be employed to a powerful predictive approach for DTIs to provide theoretical support for innovative drug discovery. [ABSTRACT FROM AUTHOR]

Objective: To investigate the effect of You-Gui Yin on glucocorticoid-induced apoptosis of rat bone marrow mesenchymal stem cells and its possible mechanism. Methods: 20 SD rats were divided into normal saline group and You-Gui Yin group. Ten rats in each group were given normal saline and You-Gui Yin by gavage for 2 weeks, once daily. After the gavage, the rats were sacrificed by spinal removal, blood was taken from the abdominal aorta and centrifuged to obtain blank serum and medicated serum. The rat bone marrow mesenchymal stem cells were extracted and cultured and administered in groups: blank group (10% blank serum), Model group (10% blank serum + dexamethasone 5×10-5mol/ml), traditional Chinese medicine group (10% medicated serum + dexamethasone 5×10-5mol/ml), control group (10% medicated serum), CCK-8 method was used to detect cell proliferation changes in different groups, ELISA method was used to detect bone alkaline phosphatase levels in each group, Alizarin red staining was used to compare red-stained calcium mineralized nodules in each group, Western Blot Detect the expression of apoptosis-related proteins in BMSCs, and perform molecular docking of the quantitative components to evaluate the binding strength and activity of the target and the active compound. Results: The ratio of absorbance (A450) in each time period of the model group was significantly reduced (P<0.05), and the ratio of absorbance (A450) between the traditional Chinese medicine group and the control group was significantly higher than that of the model group (P<0.05). There was no difference between the control group and the blank group (P>0.05); ELISA method showed that the ALP level of the model group was significantly lower than that of the blank group and the control group (P<0.05), the traditional Chinese medicine group significantly increased the ALP level (P<0.05), there was no significant difference between the control group and the blank group; Observation of the number of calcium mineralized nodules under alizarin red staining microscope suggests that the number of calcium mineralized nodules in the model group is significantly lower than that of each group, and there is no significant difference between the control group and the blank group. Both groups are higher than the model group and traditional Chinese medicine Group; Western Blot indicated that compared with the blank group, the expression levels of proapoptotic proteins Bax and Cleaved-casepase-3 in the model group were significantly increased (P<0.01), and the expression levels of anti-apoptotic protein Bcl-2 were decreased (P<0.01), on the contrary in the traditional Chinese medicine group, the expression of the control group did not change significantly compared with the blank group; the molecular docking results showed that You-Gui Yin mainly regulates the apoptosis of BMSCs through Epicatechin 5,7,3'-trimethyl ether, Delphinin, etc. promote bone formation. Conclusion: You-Gui Yin medicated serum can protect BMSCs from apoptosis induced by GCs and promote BMSCs proliferation and osteogenic differentiation by regulating Bax, Cleaved-caspase3, and Bcl-2. [ABSTRACT FROM AUTHOR]

Introduction: Parkinson’s disease (PD), which is a neurodegenerative disease, requires urgently needed biomarkers to explore its mechanism. We screened for differences in the expression of microRNAs (miRNAs) and identified miR-1976 as a possible biomarker. Methods: Twenty-three patients and 30 controls were included in this study. Dopaminergic neurons from C57/BL mice were cultured. The miRNA expression profiles were analyzed using an miRNA microarray. MiR-1976 was identified as an miRNA that was differentially expressed between PD patients and age-matched controls. Lentiviral vectors were constructed, then apoptosis in dopaminergic neurons was analyzed using MTS (multicellular tumor spheroids) and flow cytometry. Transfection of miR-1976 mimics into MES23.5 cells was performed, and target genes and biological effects were analyzed. Results: Overexpression of miR-1976 increased apoptosis and mitochondrial damage in dopaminergic neurons. PINK1 (PINK1-induced kinase 1) was the most common target protein of miR-1976, and silencing of PINK1 caused mitochondrial damage and increased apoptosis of MES23.5 cells. Conclusions: MiR-1976 is a newly discovered miRNA that exhibits a high degree of differential expression with respect to the apoptosis of dopaminergic neurons. Given these results, increased expression of miR-1976 may increase the risk of PD by targeting PINK1 and may therefore be a useful biomarker for PD.

Background: Hispolon, a phenolic compound isolated from the medicinal yellow fungal mulberry, exhibits a strong anti-triple-negative breast cancer (TNBC) effect. However, the antitumor mechanisms of Hispolon have not been fully explored., Objective: In this study, we systematically investigated the mechanism of Hispolon against TNBC based on bioinformatics and in vitro experiments., Methods: The Hispolon-related targets were first collected from the SwissTarget database. Differential Expression Genes (DEG) were screened between TNBC and normal breast tissue using the Gene Expression Comprehensive (GEO) dataset. The overlapping targets between Hispolon and DEG were analyzed by plotting Venn maps. Protein-protein interaction (PPI) network was constructed to analyze the interactions among these targets. The focus was on mining the core targets of anti-TNBC effects of Hispolon via the Cytohubba and MCODE plugin of Cytoscape 3.7.2 software. We performed survival analysis on these core targets to screen the best-matched targets, including EGFR, KIT, and PLAU. This correlated strongly with our validation of Hispolon by molecular docking. In addition, Gene Ontology (GO) anal-ysis and KEGG pathway analysis were performed using R software (ClusterProfiler package). Finally, in vitro experiments were performed to assess the accuracy of predicted target genes., Results: The ADME results suggested that Hispolon has great potential to develop into a drug. Twenty overlapping targets were screened by matching the 107 targets of Hispolon to the 2,013 targets of TNBC DEG. Seven core targets of Hispolon against TNBC were initially identified, including EGFR, IGFBP3, MMP9, MMP2, MMP1, PLAU, and KIT. GO enrich-ment analysis demonstrated that the biological process of Hispolon acting on TNBC mainly involves lymphocyte activation in immune response and phosphatidylinositol-mediated signal-ing. Additionally, the relaxin signaling pathway, estrogen signaling pathway, proteoglycans in cancer, and others might be the key pathways of Hispolon against TNBC. Furthermore, Hispo-lon inhibited the proliferation of MDA-MB-231 cells in a concentration-dependent manner and regulated the RNA and protein expression of the core targets EGFR, PLAU, and KIT for the treatment of TNBC., Conclusion: In this study, the polygenic pharmacological mechanism of action of Hispolon against TNBC was explored through network pharmacology and in vitro experiments, provid-ing a new insight into the mechanism of TCM monomer against TNBC., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Skeletal muscle plays a pivotal role in the maintenance of physical and metabolic health. Skeletal muscle atrophy usually results in physical disability, inferior quality of life and higher health care costs. The higher incidence of muscle atrophy in obese and ageing groups is due to increased levels of inflammatory factors during obesity and ageing. Dihydromyricetin, as a bioactive polyphenol, has been used for anti‐inflammatory, anti‐tumour and improving insulin sensitivity. However, there are no published reports demonstrated the dihydromyricetin effect on inflammation‐induced skeletal muscle atrophy. In this study, we first confirmed the role of dihydromyricetin in inflammation‐induced skeletal muscle atrophy in vivo and in vitro. Then, we demonstrated that dihydromyricetin resisted inflammation‐induced skeletal muscle atrophy by activating Ca2+‐CaMKK‐AMPK through signal pathway blockers, Ca2+ probes and immunofluorescence. Finally, we clarified that dihydromyricetin activated Ca2+‐CaMKK‐AMPK signalling pathway through interaction with the ryanodine receptor, its target protein, by drug affinity responsive target stability (DARTS). Our results not only demonstrated that dihydromyricetin resisted inflammation‐induced muscle atrophy via the ryanodine receptor‐CaMKK‐AMPK signal pathway but also discovered that the target protein of dihydromyricetin is the ryanodine receptor. Our results provided experimental data for the development of dihydromyricetin as a functional food and new therapeutic strategies for treating or preventing skeletal muscle atrophy. [ABSTRACT FROM AUTHOR]

By applying the mixed-ligand method, a new Co(II)-based coordination polymer with the chemical formula of {[Co2L(4,4′-bipy)0.5(H2O)] · 0.25H2O}n (1) have been successfully prepared by reaction of Co(NO3)2 · 6H2O and (benzylazanediyl)bis(methylene)-diphosphonic acid (L) with the presence of a second N-donor ligand 4,4′-bipyridine (4,4′-bipy). The treatment activity of the compound on the fracture was evaluated and the related mechanism was explored at the same time. First, the real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR) was performed to determine the relative expression levels of the cd133 in the fracture animal model after compound treatment. In addition to this, the western blotting assay was performed and the activation levels of the wnt signaling pathway in the mesenchymal stem cells was measured as well. Both nitrogen and oxygen atoms on the complex are found to be able to form interactions with target protein. [ABSTRACT FROM AUTHOR]

• Condenses key information of recently reported migration inhibitors. • Extremely useful for understanding the current research in migration inhibitors. • Provides enlightening, target-based evaluation of the potential of the inhibitors. • Provides straightforward insight into the antimigratory mechanisms of action of the inhibitors. Antimetastatic agents are highly desirable for cancer treatment because of the severe medical challenges and high mortality resulting from tumor metastasis. Having demonstrated antimetastatic effects in numerous in vitro and in vivo studies, migration inhibitors present significant opportunities for developing a new class of anticancer drugs. To provide a useful overview on the latest research in migration inhibitors, this article first discusses their therapeutic significance, targetable proteins, and developmental avenues. Subsequently it reviews over 20 representative migration inhibitors reported in recent journals in terms of their inhibitory mechanism, potency, and potential clinical utility. The relevance of the target proteins to cellular migratory function is focused on as it is crucial for assessing the overall efficacy of the inhibitors. [ABSTRACT FROM AUTHOR]

Abstract Background In silico prediction of potential drug side-effects is of crucial importance for drug development, since wet experimental identification of drug side-effects is expensive and time-consuming. Existing computational methods mainly focus on leveraging validated drug side-effect relations for the prediction. The performance is severely impeded by the lack of reliable negative training data. Thus, a method to select reliable negative samples becomes vital in the performance improvement. Methods Most of the existing computational prediction methods are essentially based on the assumption that similar drugs are inclined to share the same side-effects, which has given rise to remarkable performance. It is also rational to assume an inverse proposition that dissimilar drugs are less likely to share the same side-effects. Based on this inverse similarity hypothesis, we proposed a novel method to select highly-reliable negative samples for side-effect prediction. The first step of our method is to build a drug similarity integration framework to measure the similarity between drugs from different perspectives. This step integrates drug chemical structures, drug target proteins, drug substituents, and drug therapeutic information as features into a unified framework. Then, a similarity score between each candidate negative drug and validated positive drugs is calculated using the similarity integration framework. Those candidate negative drugs with lower similarity scores are preferentially selected as negative samples. Finally, both the validated positive drugs and the selected highly-reliable negative samples are used for predictions. Results The performance of the proposed method was evaluated on simulative side-effect prediction of 917 DrugBank drugs, comparing with four machine-learning algorithms. Extensive experiments show that the drug similarity integration framework has superior capability in capturing drug features, achieving much better performance than those based on a single type of drug property. Besides, the four machine-learning algorithms achieved significant improvement in macro-averaging F1-score (e.g., SVM from 0.655 to 0.898), macro-averaging precision (e.g., RBF from 0.592 to 0.828) and macro-averaging recall (e.g., KNN from 0.651 to 0.772) complimentarily attributed to the highly-reliable negative samples selected by the proposed method. Conclusions The results suggest that the inverse similarity hypothesis and the integration of different drug properties are valuable for side-effect prediction. The selection of highly-reliable negative samples can also make significant contributions to the performance improvement.

As the basis for screening drug candidates, the identification of drug–target interactions (DTIs) plays a crucial role in the innovative drugs research. However, due to the inherent constraints of small-scale and time-consuming wet experiments, DTI recognition is usually difficult to carry out. In the present study, we developed a computational approach called RoFDT to predict DTIs by combining feature-weighted Rotation Forest (FwRF) with a protein sequence. In particular, we first encode protein sequences as numerical matrices by Position-Specific Score Matrix (PSSM), then extract their features utilize Pseudo Position-Specific Score Matrix (PsePSSM) and combine them with drug structure information-molecular fingerprints and finally feed them into the FwRF classifier and validate the performance of RoFDT on Enzyme, GPCR, Ion Channel and Nuclear Receptor datasets. In the above dataset, RoFDT achieved 91.68%, 84.72%, 88.11% and 78.33% accuracy, respectively. RoFDT shows excellent performance in comparison with support vector machine models and previous superior approaches. Furthermore, 7 of the top 10 DTIs with RoFDT estimate scores were proven by the relevant database. These results demonstrate that RoFDT can be employed to a powerful predictive approach for DTIs to provide theoretical support for innovative drug discovery.

Marine organisms are a rich source of bioactive secondary metabolites. Although many marine natural products with bioactivities have been isolated, successful elucidation of their mechanisms of action remains limited. In this study, we prepared a probe molecule based on the marine cyclic peptide kapakahine A (1) by introducing a linker with an azide terminal group, which enables the introduction of fluorescent groups for the effective monitoring of subcellular localization, or coupling to affinity beads for the pull-down of target proteins. The results of LC/MS/MS measurements, ProteinPilot analysis, and Western blotting suggest that kapakahine A interacts with the mitochondrial inner membrane proteins PHB1, PHB2, and ANT2, which is consistent with the results of the subcellular localization analysis using a fluorescent probe.

Baicalin is a major active ingredient of traditional Chinese medicine Scutellaria baicalensis, and has been shown to have antiviral, anti-inflammatory, and antitumor activities. However, the protein targets of baicalin have remained unclear. Herein, a chemical proteomics strategy was developed by combining baicalin-functionalized magnetic nanoparticles (BCL-N3@MNPs) and quantitative mass spectrometry to identify the target proteins of baicalin. Bioinformatics analysis with the use of Gene Ontology, STRING and Ingenuity Pathway Analysis, was performed to annotate the biological functions and the associated signaling pathways of the baicalin targeting proteins. Fourteen proteins in human embryonic kidney cells were identified to interact with baicalin with various binding affinities. Bioinformatics analysis revealed these proteins are mainly ATP-binding and/or ATPase activity proteins, such as CKB, HSP86, HSP70-1, HSP90, ATPSF1β and ACTG1, and highly associated with the regulation of the role of PKR in interferon induction and the antiviral response signaling pathway (P = 10−6), PI3K/AKT signaling pathway (P = 10−5) and eNOS signaling pathway (P = 10−4). The results show that baicalin exerts multiply pharmacological functions, such as antiviral, anti-inflammatory, antitumor, and antioxidant functions, through regulating the PKR and PI3K/AKT/eNOS signaling pathways by targeting ATP-binding and ATPase activity proteins. These findings provide a fundamental insight into further studies on the mechanism of action of baicalin.

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

Abscisic acid (ABA, 1) is a plant hormone that regulates various plant physiological processes such as seed developing and stress responses. The ABA signaling system has been elucidated; binding of ABA with PYL proteins triggers ABA signaling. We have previously reported a new method to isolate a protein targeted with a bioactive small molecule using a biotin linker with alkyne and amino groups, a protein cross-linker, and a bioactive small molecule with an azido group (azido probe). This method was used to identify the unknown ABA binding protein of Arabidopsis thaliana. As a result, AtTrxh3, a thioredoxin, was isolated as an ABA binding protein. Our developed method can be applied to the identification of binding proteins of bioactive compounds.

The present study is an attempt to evaluate the in vitro anti‐inflammatory and in silico anticancer potentials of the plant Cassia auriculata (CA). The aerial parts of CA were subjected to solvent extraction, and the extracts were fractionised by gas chromatography and mass spectrometry analysis for its phytochemical content. The antiinflammatory activity of the extracts were confirmed by the IC50 value of 125.02 µg/ml for red blood cell membrane stabilisation and 195.7 µg/ml for inhibition of protein denaturation activity. The interaction of bioactive compounds of CA ethanol extract with target protein was predicted through molecular docking studies, serine/threonine–protein kinase B (AKT1), responsible for development and progression of lung cancer using AutoDock tools. Extensive studies have been carried out on a range of kinase inhibitors targeting Akt, but obtaining promising results is a challenge yet due to its toxicity and resistance issues. Yohimbine, undecanoic acid 10‐methyl‐ethyl ester and chrysin significantly bind to the target protein with least binding energy. Hence, the present paper establishes the anti‐inflammatory and anticancer capacities of CA ethanol extract as an alternative to the existing therapeutic approach to inflammation and cancer through a systematic in vitro and in silico approaches supplementing the findings. [ABSTRACT FROM AUTHOR]

Blocking the biological functions of scaffold proteins and aggregated proteins is a challenging goal. PROTAC proteolysis-targeting chimaera (PROTAC) technology may be the solution, considering its ability to selectively degrade target proteins. Recent progress in the PROTAC strategy include identification of the structure of the first ternary eutectic complex, extra-terminal domain-4-PROTAC-Von-Hippel-Lindau (BRD4-PROTAC-VHL), and PROTAC ARV-110 has entered clinical trials for the treatment of prostate cancer in 2019. These discoveries strongly proved the value of the PROTAC strategy. In this perspective, we summarized recent meaningful research of PROTAC, including the types of degradation proteins, preliminary biological data in vitro and in vivo, and new E3 ubiquitin ligases. Importantly, the molecular design, optimization strategy and clinical application of candidate molecules are highlighted in detail. Future perspectives for development of advanced PROTAC in medical fields have also been discussed systematically. Strategies for protein degradation include simulating misfolded proteins through hydrophobic tagging; causing proteins to be hijacked by E3 ubiquitin ligase and ubiquitinated through proteolysis-targeting chimaeras (PROTAC). Stable PROTAC ternary complex, which forms new protein–protein interactions (PPIs) by protein with E3 ligase, is essential for protein degradation. Image 1 [ABSTRACT FROM AUTHOR]

The increasing resistance displayed by plant phytopathogenic bacteria to conventional pesticides has heightened the urgency for the exploration of novel antibacterial agents possessing distinct modes of action (MOAs). In this study, a series of novel phenylalanine derivatives with the unique structure of acylhydrazone dithioether have been designed and synthesized. Bioassay results demonstrated that most target compounds exhibited excellent in vitro antibacterial activity against Xanthomonas oryzae pv oryzae ( Xoo ) and Xanthomonas axonopodis pv citri ( Xac ). Among them, the EC 50 values of L 3 , L 4 , L 6 , L 21 , and L 22 against Xoo were 7.4, 9.3, 6.7, 8.9, and 5.1 μg/mL, respectively, superior to that of bismerthiazol (BT) and thiodiazole copper (TC) (41.5 and >100 μg/mL); the EC 50 values of L 3 , L 4 , L 5 , and the 50S ribosomal protein L2 (RL2) as an unprecedented target protein in L cells was first discovered. The target protein RL2 was then expressed and purified. Furthermore, the 6 , L 7 , L 8 , L 20 , L 21 , and L 22 against Xac were 5.6, 2.5, 6.2, 4.1, 4.2, 6.4, 6.3, 3.6, and 5.2 μg/mL, respectively, superior to that of BT and TC (43.3 and >100 μg/mL). An unmodified drug affinity responsive target stability (DARTS) technology was used to investigate the antibacterial MOAs of active compound L 22 , and the 50S ribosomal protein L2 (RL2) as an unprecedented target protein in Xoo cells was first discovered. The target protein RL2 was then expressed and purified. Furthermore, the in vitro interactions by microscale thermophoresis ( K d = 0.050 μM) and fluorescence titration ( K a = 1.4 × 10 5 M -1 ) experiments also demonstrated a strong binding force between compound L 22 and RL2. Overall, these results not only facilitate the development of novel antibacterial agents but also establish a reliable method for exploring the targets of bactericides.

We previously reported that bakuchiol, a phenolic isoprenoid anticancer compound, and its analogs exert anti-influenza activity. However, the proteins targeted by bakuchiol remain unclear. Here, we investigated the chemical structures responsible for the anti-influenza activity of bakuchiol and found that all functional groups and C6 chirality of bakuchiol were required for its anti-influenza activity. Based on these results, we synthesized a molecular probe containing a biotin tag bound to the C1 position of bakuchiol. With this probe, we performed a pulldown assay for Madin-Darby canine kidney cell lysates and purified the specific bakuchiol-binding proteins with SDS-PAGE. Using nanoLC-MS/MS analysis, we identified prohibitin (PHB) 2, voltage-dependent anion channel (VDAC) 1, and VDAC2 as binding proteins of bakuchiol. We confirmed the binding of bakuchiol to PHB1, PHB2, and VDAC2 in vitro using Western blot analysis. Immunofluorescence analysis showed that bakuchiol was bound to PHBs and VDAC2 in cells and colocalized in the mitochondria. The knockdown of PHBs or VDAC2 by transfection with specific siRNAs, along with bakuchiol cotreatment, led to significantly reduced influenza nucleoprotein expression levels and viral titers in the conditioned medium of virus-infected Madin-Darby canine kidney cells, compared to the levels observed with transfection or treatment alone. These findings indicate that reducing PHBs or VDAC2 protein, combined with bakuchiol treatment, additively suppressed the growth of influenza virus. Our findings indicate that bakuchiol exerts anti-influenza activity via a novel mechanism involving these mitochondrial proteins, providing new insight for developing anti-influenza agents., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest regarding the content of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

An estimated 240 fungicides are presently in use, but the direct targets for the majority remain elusive, constraining fungicide development and efficient resistance monitoring. In this study, we found that Pcα-actinin knockout did not influence the sensitivity of Phytophthora capsici to fluopicolide, which is a notable oomycete inhibitor. Using a combination of Bulk Segregant Analysis Sequencing and Drug Affinity Responsive Target Stability (DARTS) assays, the vacuolar H + -ATPase subunit a (PcVHA-a) was pinpointed as the target protein of fluopicolide. We also confirmed four distinct point mutations in PcVHA-a responsible for fluopicolide resistance in P. capsici through site-directed mutagenesis. Molecular docking, ATPase activity assays, and a DARTS assay suggested a fluopicolide-PcVHA-a interaction. Sequence analysis and further molecular docking validated the specificity of fluopicolide for oomycetes or fish. These findings support the claim that PcVHA-a is the target of fluopicolide, proposing vacuolar H + -ATPase as a promising target for novel fungicide development.

Introduction: Carnosol exhibited ameliorating effects on muscle atrophy of mice developed cancer cachexia in our previous research. Method: Here, the ameliorating effects of carnosol on the C2C12 myotube atrophy result from simulated cancer cachexia injury, the conditioned medium of the C26 tumor cells or the LLC tumor cells, were observed. To clarify the mechanisms of carnosol, the possible direct target proteins of carnosol were searched using DARTS (drug affinity responsive target stability) assay and then confirmed using CETSA (cellular thermal shift assay). Furthermore, proteomic analysis was used to search its possible indirect target proteins by comparing the protein expression profiles of C2C12 myotubes under treatment of C26 medium, with or without the presence of carnosol. The signal network between the direct and indirect target proteins of carnosol was then constructed. Results: Our results showed that, Delta-1-pyrroline-5-carboxylate synthase (P5CS) might be the direct target protein of carnosol in myotubes. The influence of carnosol on amino acid metabolism downstream of P5CS was confirmed. Carnosol could upregulate the expression of proteins related to glutathione metabolism, anti-oxidant system, and heat shock response. Knockdown of P5CS could also ameliorate myotube atrophy and further enhance the ameliorating effects of carnosol. Discussion: These results suggested that carnosol might ameliorate cancer cachexia-associated myotube atrophy by targeting P5CS and its downstream pathways., Competing Interests: Authors L-XF was employed by Shanghai Majorbio Bio-Pharm Technology Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Fang, Wang, Zhang, Fan, Feng, Guo, Cheng, Zhang and Liu.)

Background: In silico prediction of potential drug side-effects is of crucial importance for drug development, since wet experimental identification of drug side-effects is expensive and time-consuming. Existing computational methods mainly focus on leveraging validated drug side-effect relations for the prediction. The performance is severely impeded by the lack of reliable negative training data. Thus, a method to select reliable negative samples becomes vital in the performance improvement. Methods: Most of the existing computational prediction methods are essentially based on the assumption that similar drugs are inclined to share the same side-effects, which has given rise to remarkable performance. It is also rational to assume an inverse proposition that dissimilar drugs are less likely to share the same side-effects. Based on this inverse similarity hypothesis, we proposed a novel method to select highly-reliable negative samples for side-effect prediction. The first step of our method is to build a drug similarity integration framework to measure the similarity between drugs from different perspectives. This step integrates drug chemical structures, drug target proteins, drug substituents, and drug therapeutic information as features into a unified framework. Then, a similarity score between each candidate negative drug and validated positive drugs is calculated using the similarity integration framework. Those candidate negative drugs with lower similarity scores are preferentially selected as negative samples. Finally, both the validated positive drugs and the selected highly-reliable negative samples are used for predictions. Results: The performance of the proposed method was evaluated on simulative side-effect prediction of 917 DrugBank drugs, comparing with four machine-learning algorithms. Extensive experiments show that the drug similarity integration framework has superior capability in capturing drug features, achieving much better performance than those based on a single type of drug property. Besides, the four machine-learning algorithms achieved significant improvement in macro-averaging F1-score (e.g., SVM from 0.655 to 0.898), macro-averaging precision (e.g., RBF from 0.592 to 0.828) and macro-averaging recall (e.g., KNN from 0.651 to 0.772) complimentarily attributed to the highly-reliable negative samples selected by the proposed method. Conclusions: The results suggest that the inverse similarity hypothesis and the integration of different drug properties are valuable for side-effect prediction. The selection of highly-reliable negative samples can also make significant contributions to the performance improvement. [ABSTRACT FROM AUTHOR]

The function of drugs is based on the interaction between drug molecules and their targets. Qualitative analysis and quantitative detection of drug-target interactions run through the whole process from drug discovery to clinical practice. After decades of development, the study methods on the interaction between drug molecules and target proteins have been transformed from traditional biochemical experiments to a diversity of efficient and accurate technology systems supported by advanced molecular biology and biophysics theory. In this review, representative methods and techniques were introduced from aspects of target discovery and validation,affinity determination, interaction sites and structural analysis, which might provide some references for drug discovery and mechanism exploration. [ABSTRACT FROM AUTHOR]