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  • Oxford University Press (OUP)  (1,061)
  • 1
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    PTMdyna: exploring the influence of post-translation modifications on protein conformational dynamics
    Oxford University Press (OUP) ; 2022
    In:  Briefings in Bioinformatics Vol. 23, No. 1 ( 2022-01-17)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 23, No. 1 ( 2022-01-17)
    Abstract: Protein post-translational modifications (PTM) play vital roles in cellular regulation, modulating functions by driving changes in protein structure and dynamics. Exploring comprehensively the influence of PTM on conformational dynamics can facilitate the understanding of the related biological function and molecular mechanism. Currently, a series of excellent computation tools have been designed to analyze the time-dependent structural properties of proteins. However, the protocol aimed to explore conformational dynamics of post-translational modified protein is still a blank. To fill this gap, we present PTMdyna to visually predict the conformational dynamics differences between unmodified and modified proteins, thus indicating the influence of specific PTM. PTMdyna exhibits an AUC of 0.884 tested on 220 protein–protein complex structures. The case of heterochromatin protein 1α complexed with lysine 9-methylated histone H3, which is critical for genomic stability and cell differentiation, was used to demonstrate its applicability. PTMdyna provides a reliable platform to predict the influence of PTM on protein dynamics, making it easier to interpret PTM functionality at the structure level. The web server is freely available at http://ccbportal.com/PTMdyna.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbab424
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2036055-1
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  • 2
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    Exploring the kinase-inhibitor fragment interaction space facilitates the discovery of kinase inhibitor overcoming resistance by mutations
    Oxford University Press (OUP) ; 2022
    In:  Briefings in Bioinformatics Vol. 23, No. 4 ( 2022-07-18)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 23, No. 4 ( 2022-07-18)
    Abstract: Protein kinases play crucial roles in many cellular signaling processes, making them become important targets for drug discovery. But drug resistance mediated by mutation puts a barrier to the therapeutic effect of kinase inhibitors. Fragment-based drug discovery has been successfully applied to overcome such resistance. However, the complicate kinase-inhibitor fragment interaction and fragment-to-lead process seriously limit the efficiency of kinase inhibitor discovery against resistance caused by mutation. Here, we constructed a comprehensive web platform KinaFrag for the fragment-based kinase inhibitor discovery to overcome resistance. The kinase-inhibitor fragment space was investigated from 7783 crystal kinase-inhibitor fragment complexes, and the structural requirements of kinase subpockets were analyzed. The core fragment-based virtual screening workflow towards specific subpockets was developed to generate new kinase inhibitors. A series of tropomyosin receptor kinase (TRK) inhibitors were designed, and the most potent compound YT9 exhibits up to 70-fold activity improvement than marketed drugs larotrectinib and selitrectinib against G595R, G667C and F589L mutations of TRKA. YT9 shows promising antiproliferative against tumor cells in vitro and effectively inhibits tumor growth in vivo for wild type TRK and TRK mutants. Our results illustrate the great potential of KinaFrag in the kinase inhibitor discovery to combat resistance mediated by mutation. KinaFrag is freely available at http://chemyang.ccnu.edu.cn/ccb/database/KinaFrag/.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbac203
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 3
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    ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy
    Oxford University Press (OUP) ; 2023
    In:  Nucleic Acids Research Vol. 51, No. W1 ( 2023-07-05), p. W25-W32
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 51, No. W1 ( 2023-07-05), p. W25-W32
    Abstract: Drug discovery, which plays a vital role in maintaining human health, is a persistent challenge. Fragment-based drug discovery (FBDD) is one of the strategies for the discovery of novel candidate compounds. Computational tools in FBDD could help to identify potential drug leads in a cost-efficient and time-saving manner. The Auto Core Fragment in silico Screening (ACFIS) server is a well-established and effective online tool for FBDD. However, the accurate prediction of protein-fragment binding mode and affinity is still a major challenge for FBDD due to weak binding affinity. Here, we present an updated version (ACFIS 2.0), that incorporates a dynamic fragment growing strategy to consider protein flexibility. The major improvements of ACFIS 2.0 include (i) increased accuracy of hit compound identification (from 75.4% to 88.5% using the same test set), (ii) improved rationality of the protein-fragment binding mode, (iii) increased structural diversity due to expanded fragment libraries and (iv) inclusion of more comprehensive functionality for predicting molecular properties. Three successful cases of drug lead discovery using ACFIS 2.0 are described, including drugs leads to treat Parkinson's disease, cancer, and major depressive disorder. These cases demonstrate the utility of this web-based server. ACFIS 2.0 is freely available at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS2/.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkad348
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 4
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    Cloud 3D-QSAR: a web tool for the development of quantitative structure–activity relationship models in drug discovery
    Oxford University Press (OUP) ; 2021
    In:  Briefings in Bioinformatics Vol. 22, No. 4 ( 2021-07-20)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 22, No. 4 ( 2021-07-20)
    Abstract: Effective drug discovery contributes to the treatment of numerous diseases but is limited by high costs and long cycles. The Quantitative Structure–Activity Relationship (QSAR) method was introduced to evaluate the activity of a large number of compounds virtually, reducing the time and labor costs required for chemical synthesis and experimental determination. Hence, this method increases the efficiency of drug discovery. To meet the needs of researchers to utilize this technology, numerous QSAR-related web servers, such as Web-4D-QSAR and DPubChem, have been developed in recent years. However, none of the servers mentioned above can perform a complete QSAR modeling and supply activity prediction functions. We introduce Cloud 3D-QSAR by integrating the functions of molecular structure generation, alignment, molecular interaction field (MIF) computing and results analysis to provide a one-stop solution. We rigidly validated this server, and the activity prediction correlation was R2 = 0.934 in 834 test molecules. The sensitivity, specificity and accuracy were 86.9%, 94.5% and 91.5%, respectively, with AUC = 0.981, AUCPR = 0.971. The Cloud 3D-QSAR server may facilitate the development of good QSAR models in drug discovery. Our server is free and now available at http://chemyang.ccnu.edu.cn/ccb/server/cloud3dQSAR/ and http://agroda.gzu.edu.cn:9999/ccb/server/cloud3dQSAR/.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbaa276
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2036055-1
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  • 5
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    Resistance Risk Evaluated by Metaflumizone Selection and the Effects on Toxicities Over Other Insecticides in Spodoptera exigua (Lepidoptera: Noctuidae)
    Oxford University Press (OUP) ; 2019
    In:  Journal of Economic Entomology Vol. 112, No. 5 ( 2019-09-23), p. 2354-2361
    Details
    In: Journal of Economic Entomology, Oxford University Press (OUP), Vol. 112, No. 5 ( 2019-09-23), p. 2354-2361
    Abstract: Metaflumizone is a novel semicarbazone insecticide. It functions as a sodium channel blocker insecticide (SCBI) with excellent insecticidal activity on most economically important lepidopterous pests. This study assessed the resistance risk of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae) to metaflumizone in the laboratory and the effects of metaflumizone selection on toxicities to other insecticides. Spodoptera exigua collected from a field population at Huizhou in 2012 were successively challenged by metaflumizone to evaluate the risk of resistance evolution. Twelve generations of selection increased resistance to metaflumizone by 3.4-fold and threshold trait analysis revealed that the realized heritability (h2) of this resistance was 0.086. When h2 was equal to 0.086 and 90% of individuals were killed at each generation, LC50 to metaflumizone increased by 10-fold after 15 generations. The selection by metaflumizone did not increase the resistance to indoxacarb, chlorantraniliprole, spinosad, methomyl, or endosulfan, suggesting a lack of cross-resistance. However, metaflumizone challenge upheld the recession of resistance to emamectin benzoate, chlorfluazuron, and tebufenozide. The block of resistance drops by metaflumizone exposure implied a possible cross-resistance between metaflumizone and these three insecticides. These results contribute to integrated resistance management of S. exigua.
    Type of Medium: Online Resource
    ISSN: 0022-0493 , 1938-291X
    URL: Article
    DOI: 10.1093/jee/toz171
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2477182-X
    detail.hit.zdb_id: 2030999-5
    SSG: 12
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  • 6
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    2.5-D frequency-domain viscoelastic wave modelling using finite-element method
    Oxford University Press (OUP) ; 2017
    In:  Geophysical Journal International Vol. 211, No. 1 ( 2017-10), p. 164-187
    Details
    In: Geophysical Journal International, Oxford University Press (OUP), Vol. 211, No. 1 ( 2017-10), p. 164-187
    Type of Medium: Online Resource
    ISSN: 0956-540X , 1365-246X
    URL: Article
    DOI: 10.1093/gji/ggx273
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
    detail.hit.zdb_id: 3042-9
    detail.hit.zdb_id: 2006420-2
    detail.hit.zdb_id: 1002799-3
    SSG: 16,13
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  • 7
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    Compound shougong powder inhibits the malignant phenotype of hepatocellular carcinoma cells by targeting the DNA damage repair pathway
    Oxford University Press (OUP) ; 2023
    In:  Journal of Pharmacy and Pharmacology Vol. 75, No. 5 ( 2023-04-17), p. 703-711
    Details
    In: Journal of Pharmacy and Pharmacology, Oxford University Press (OUP), Vol. 75, No. 5 ( 2023-04-17), p. 703-711
    Abstract: Compound Shougong Powder (SGS), a traditional Chinese medicine formulation, has been used to treat cancer for many years with remarkable efficacy. However, the mechanisms underlying the therapeutic effect of SGS in Hepatocellular carcinoma (HCC) are not completely clear. Methods The survival and metastasis of HCC cells were examined by CCK-8 assay, EdU assay, Wound-healing and Transwell assay. The anti-tumour effect of SGS was studied using hoechst 33258 staining and flow cytometry. RNA sequencing was applied to detect the underlying mechanism. Comet DNA, qRT-PCR and WB experiments were performed for validation. In addition, HCC nude mouse model was constructed to detect SGS effect in vivo. Key findings SGS inhibited the proliferation, migration and invasion of HCC cells and induced apoptosis in vitro. In addition, SGS also suppressed tumour growth in a nude mouse model of HCC in a dose-dependent manner. RNA sequencing of the suitably treated HCC cells revealed significant changes in the expression levels of genes involved in the DNA damage repair pathway. The sequencing results were verified by Comet DNA, qRT-PCR, WB assays and molecular docking. Conclusions Taken together, SGS inhibits the malignant phenotype of HCC cells by down-regulating DNA repair genes and consequently inducing DNA damage.
    Type of Medium: Online Resource
    ISSN: 0022-3573 , 2042-7158
    URL: Article
    DOI: 10.1093/jpp/rgad026
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2041988-0
    detail.hit.zdb_id: 2050532-2
    SSG: 15,3
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  • 8
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    Detection of bla NDM-1 in Moellerella wisconsensis from mutton, China
    Oxford University Press (OUP) ; 2023
    In:  Journal of Antimicrobial Chemotherapy Vol. 78, No. 10 ( 2023-10-03), p. 2599-2601
    Details
    In: Journal of Antimicrobial Chemotherapy, Oxford University Press (OUP), Vol. 78, No. 10 ( 2023-10-03), p. 2599-2601
    Type of Medium: Online Resource
    ISSN: 0305-7453 , 1460-2091
    URL: Article
    DOI: 10.1093/jac/dkad222
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1467478-6
    SSG: 15,3
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  • 9
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    First-line Therapy With Donor-derived Human Cytomegalovirus (HCMV)–specific T Cells Reduces Persistent HCMV Infection by Promoting Antiviral Immunity After Allogenic Stem Cell Transplantation
    Oxford University Press (OUP) ; 2020
    In:  Clinical Infectious Diseases Vol. 70, No. 7 ( 2020-03-17), p. 1429-1437
    Details
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 70, No. 7 ( 2020-03-17), p. 1429-1437
    Abstract: Human cytomegalovirus (HCMV) infection, especially persistent HCMV infection, is an important cause of morbidity and mortality after allogenic stem cell transplantation (allo-SCT). Antiviral agents remain the first-line therapy but are limited by side effects and acquired resistance. Methods We evaluated the safety and efficacy of donor-derived HCMV-specific cytotoxic T cells (CTLs) as a first-line therapy for HCMV infection after allo-SCT and investigated the underlying mechanisms. Results In humanized HCMV-infected mice, first-line therapy with CTLs effectively combated systemic HCMV infection by promoting the restoration of graft-derived endogenous HCMV-specific immunity in vivo. In a clinical trial, compared with the pair-matched, high-risk control cohort, first-line therapy with CTLs significantly reduced the rate of persistent (2.9% vs 20.0%, P = .018) and late (5.7% vs 20.0%, P = .01) HCMV infection and cumulative incidence of persistent HCMV infection (hazard ratio [HR], 0.13; 95% confidence interval [CI] , 0.10–0.82; P = .02), lowered 1-year treatment-related mortality (HR, 0.15. 95% CI, 0.11–0.90. P = .03), and improved 1-year overall survival (HR, 6.35; 95% CI, 1.05–9.00; P = .04). Moreover, first-line therapy with CTLs promoted the quantitative and functional recovery of CTLs in patients, which was associated with HCMV clearance. Conclusions We provide robust support for the benefits of CTLs combined with antiviral drugs as a first-line therapy for treating HCMV infection and suggest that adoptively infused CTLs may stimulate the recovery of endogenous HCMV-specific immunity. Clinical trials registration NCT02985775.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    URL: Article
    DOI: 10.1093/cid/ciz368
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2002229-3
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  • 10
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    Citrus ACC synthase CiACS4 regulates plant height by inhibiting gibberellin biosynthesis
    Oxford University Press (OUP) ; 2023
    In:  Plant Physiology Vol. 192, No. 3 ( 2023-07-03), p. 1947-1968
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 192, No. 3 ( 2023-07-03), p. 1947-1968
    Abstract: Dwarfism is an agronomic trait that has substantial effects on crop yield, lodging resistance, planting density, and a high harvest index. Ethylene plays an important role in plant growth and development, including the determination of plant height. However, the mechanism by which ethylene regulates plant height, especially in woody plants, remains unclear. In this study, a 1-aminocyclopropane-1-carboxylic acid synthase (ACC) gene (ACS), which is involved in ethylene biosynthesis, was isolated from lemon (Citrus limon L. Burm) and named CiACS4. Overexpression of CiACS4 resulted in a dwarf phenotype in Nicotiana tabacum and lemon and increased ethylene release and decreased gibberellin (GA) content in transgenic plants. Inhibition of CiACS4 expression in transgenic citrus significantly increased plant height compared with the controls. Yeast two-hybrid assays revealed that CiACS4 interacted with an ethylene response factor (ERF), CiERF3. Further experiments revealed that the CiACS4–CiERF3 complex can bind to the promoters of 2 citrus GA20-oxidase genes, CiGA20ox1 and CiGA20ox2, and suppress their expression. In addition, another ERF transcription factor, CiERF023, identified using yeast one-hybrid assays, promoted CiACS4 expression by binding to its promoter. Overexpression of CiERF023 in N. tabacum caused a dwarfing phenotype. CiACS4, CiERF3, and CiERF023 expression was inhibited and induced by GA3 and ACC treatments, respectively. These results suggest that the CiACS4–CiERF3 complex may be involved in the regulation of plant height by regulating CiGA20ox1 and CiGA20ox2 expression levels in citrus.
    Type of Medium: Online Resource
    ISSN: 0032-0889 , 1532-2548
    URL: Article
    DOI: 10.1093/plphys/kiad159
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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