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      Syrbactin-class dual constitutive- and immuno-proteasome inhibitor TIR-199 impedes myeloma-mediated bone degeneration in vivo

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          Abstract

          Proteasome-addicted neoplastic malignancies present a considerable refractory and relapsed phenotype with patients exhibiting drug resistance and high mortality rates. To counter this global problem, novel proteasome-based therapies are being developed. In the current study, we extensively characterize TIR-199, a syrbactin-class proteasome inhibitor derived from a plant virulence factor of bacterium Pseudomonas syringae pv syringae. We report that TIR-199 is a potent constitutive and immunoproteasome inhibitor, capable of inducing cell death in multiple myeloma, triple-negative breast cancer, (TNBC) and non-small cell lung cancer lines. TIR-199 also effectively inhibits the proteasome in primary myeloma cells of patients, and bypasses the PSMB5 A49T+A50V bortezomib-resistant mutant. TIR-199 treatment leads to accumulation of canonical proteasome substrates in cells, it is specific, and does not inhibit 50 other enzymes tested in vitro. The drug exhibits synergistic cytotoxicity in combination with proteasome-activating kinase DYRK2 inhibitor LDN192960. Furthermore, low-doses of TIR-199 exhibits in vivo activity by delaying myeloma-mediated bone degeneration in a mouse xenograft model. Together, our data indicates that proteasome inhibitor TIR-199 could indeed be a promising next-generation drug within the repertoire of proteasome-based therapeutics.

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          AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

          AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. Copyright 2009 Wiley Periodicals, Inc.
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            Guidelines for assessment of bone microstructure in rodents using micro-computed tomography.

            Use of high-resolution micro-computed tomography (microCT) imaging to assess trabecular and cortical bone morphology has grown immensely. There are several commercially available microCT systems, each with different approaches to image acquisition, evaluation, and reporting of outcomes. This lack of consistency makes it difficult to interpret reported results and to compare findings across different studies. This article addresses this critical need for standardized terminology and consistent reporting of parameters related to image acquisition and analysis, and key outcome assessments, particularly with respect to ex vivo analysis of rodent specimens. Thus the guidelines herein provide recommendations regarding (1) standardized terminology and units, (2) information to be included in describing the methods for a given experiment, and (3) a minimal set of outcome variables that should be reported. Whereas the specific research objective will determine the experimental design, these guidelines are intended to ensure accurate and consistent reporting of microCT-derived bone morphometry and density measurements. In particular, the methods section for papers that present microCT-based outcomes must include details of the following scan aspects: (1) image acquisition, including the scanning medium, X-ray tube potential, and voxel size, as well as clear descriptions of the size and location of the volume of interest and the method used to delineate trabecular and cortical bone regions, and (2) image processing, including the algorithms used for image filtration and the approach used for image segmentation. Morphometric analyses should be based on 3D algorithms that do not rely on assumptions about the underlying structure whenever possible. When reporting microCT results, the minimal set of variables that should be used to describe trabecular bone morphometry includes bone volume fraction and trabecular number, thickness, and separation. The minimal set of variables that should be used to describe cortical bone morphometry includes total cross-sectional area, cortical bone area, cortical bone area fraction, and cortical thickness. Other variables also may be appropriate depending on the research question and technical quality of the scan. Standard nomenclature, outlined in this article, should be followed for reporting of results. 2010 American Society for Bone and Mineral Research.
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              Structure and functions of the 20S and 26S proteasomes.

              The proteasome is an essential component of the ATP-dependent proteolytic pathway in eukaryotic cells and is responsible for the degradation of most cellular proteins. The 20S (700-kDa) proteasome contains multiple peptidase activities that function through a new type of proteolytic mechanism involving a threonine active site. The 26S (2000-kDa) complex, which degrades ubiquitinated proteins, contains in addition to the 20S proteasome a 19S regulatory complex composed of multiple ATPases and components necessary for binding protein substrates. The proteasome has been highly conserved during eukaryotic evolution, and simpler forms are even found in archaebacteria and eubacteria. Major advances have been achieved recently in our knowledge about the molecular organization of the 20S and 19S particles, their subunits, the proteasome's role in MHC-class 1 antigen presentation, and regulators of its activities. This article focuses on recent progress concerning the biochemical mechanisms and intracellular functions of the 20S and 26S proteasomes.
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                Author and article information

                Contributors
                Role: Formal analysisRole: ValidationRole: InvestigationRole: VisualizationRole: MethodologyRole: Writing—original draftRole: Writing—review & editing
                Role: ResourcesRole: Data curationRole: SoftwareRole: Formal analysisRole: ValidationRole: InvestigationRole: VisualizationRole: MethodologyRole: Writing—review & editing
                Role: ResourcesRole: Data curationRole: SoftwareRole: Formal analysisRole: ValidationRole: InvestigationRole: VisualizationRole: MethodologyRole: Writing—original draft
                Role: ResourcesRole: Data curationRole: SoftwareRole: SupervisionRole: ValidationRole: InvestigationRole: VisualizationRole: Methodology
                Role: SupervisionRole: Funding acquisitionRole: Methodology
                Role: Resources
                Role: SupervisionRole: Funding acquisitionRole: Formal analysisRole: ValidationRole: InvestigationRole: VisualizationRole: MethodologyRole: Writing—original draftRole: Writing—review & editing
                Journal
                Biosci Rep
                Biosci Rep
                bsr
                Bioscience Reports
                Portland Press Ltd.
                0144-8463
                1573-4935
                25 February 2022
                11 February 2022
                : 42
                : 2
                : BSR20212721
                Affiliations
                [1 ]Department of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, U.K.
                [2 ]Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar 388120, Gujarat, India
                [3 ]Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A.
                [4 ]Department of Chemistry, University of California, Riverside, CA 92521, U.S.A.
                [5 ]Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, U.S.A.
                Author notes
                Correspondence: Sourav Banerjee ( s.y.banerjee@ 123456dundee.ac.uk )
                Author information
                https://orcid.org/0000-0003-2043-2989
                Article
                BSR20212721
                10.1042/BSR20212721
                8837819
                35088066
                77c4cea1-a91e-4ffb-b1a2-c01aa5599775
                © 2022 The Author(s).

                This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY). Open access for this article was enabled by the participation of University of Dundee in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society under a transformative agreement with JISC.

                History
                : 01 December 2021
                : 10 January 2022
                : 27 January 2022
                : 28 January 2022
                Page count
                Pages: 13
                Categories
                Cancer
                Molecular Bases of Health & Disease
                Pharmacology & Toxicology
                Signaling
                Research Articles

                Life sciences
                breast cancers,cancer,drug resistance,enzyme activity,multiple myeloma,proteasome inhibitor

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