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  1. Article ; Online: Function and Chemotypes of Human Hsp70 Chaperones.

    Shrestha, Liza / Young, Jason C

    Current topics in medicinal chemistry

    2016  Volume 16, Issue 25, Page(s) 2812–2828

    Abstract: In humans, Hsp70 chaperones are ubiquitously expressed in the cytosol, endoplasmic reticulum and mitochondria. They fulfill important roles in protein folding and the protection of cells from stress. Different forms of Hsp70 have also been found to ... ...

    Abstract In humans, Hsp70 chaperones are ubiquitously expressed in the cytosol, endoplasmic reticulum and mitochondria. They fulfill important roles in protein folding and the protection of cells from stress. Different forms of Hsp70 have also been found to regulate specific signaling pathways, many related to cell death. Cancer cells are notably abnormally dependent on Hsp70 chaperones for their survival. The importance of Hsp70s as drug targets is increasingly being recognized, particularly as potential cancer therapeutics. This review surveys recent advances in understanding Hsp70 mechanisms and then moves to provide an overview of current efforts directed at inhibiting Hsp70s as a target in diseases such as cancer and neurodegenerative disease.
    MeSH term(s) Animals ; Cell Death ; HSP70 Heat-Shock Proteins/chemistry ; HSP70 Heat-Shock Proteins/physiology ; Humans ; Neoplasms/physiopathology ; Oxidative Stress ; Structure-Activity Relationship
    Chemical Substances HSP70 Heat-Shock Proteins
    Language English
    Publishing date 2016-04-12
    Publishing country United Arab Emirates
    Document type Journal Article ; Review
    ZDB-ID 2064823-6
    ISSN 1873-4294 ; 1568-0266
    ISSN (online) 1873-4294
    ISSN 1568-0266
    DOI 10.2174/1568026616666160413142028
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  2. Article: Integration and evaluation of chest X-ray artificial intelligence in clinical practice.

    Wong, Koon-Pong / Homer, Suzanne Y / Wei, Sindy H / Yaghmai, Nazanin / Estrada Paz, Oscar A / Young, Timothy J / Buhr, Russell G / Barjaktarevic, Igor / Shrestha, Liza / Daly, Morgan / Goldin, Jonathan / Enzmann, Dieter R / Brown, Matthew S

    Journal of medical imaging (Bellingham, Wash.)

    2023  Volume 10, Issue 5, Page(s) 51805

    Abstract: Purpose: To integrate and evaluate an artificial intelligence (AI) system that assists in checking endotracheal tube (ETT) placement on chest x-rays (CXRs) in clinical practice.: Approach: In clinical use over 17 months, 214 CXR images were ordered ... ...

    Abstract Purpose: To integrate and evaluate an artificial intelligence (AI) system that assists in checking endotracheal tube (ETT) placement on chest x-rays (CXRs) in clinical practice.
    Approach: In clinical use over 17 months, 214 CXR images were ordered to check ETT placement with AI assistance by intensive care unit (ICU) physicians. The system was built on the SimpleMind Cognitive AI platform and integrated into a clinical workflow. It automatically identified the ETT and checked its placement relative to the trachea and carina. The ETT overlay and misplacement alert messages generated by the AI system were compared with radiology reports as the reference. A survey study was also conducted to evaluate usefulness of the AI system in clinical practice.
    Results: The alert messages indicating that either the ETT was misplaced or not detected had a positive predictive value of 42% (21/50) and negative predictive value of 98% (161/164) based on the radiology reports. In the survey, radiologist and ICU physician users indicated that they agreed with the AI outputs and that they were useful.
    Conclusions: The AI system performance in real-world clinical use was comparable to that seen in previous experiments. Based on this and physician survey results, the system can be deployed more widely at our institution, using insights gained from this evaluation to make further algorithm improvements and quality assurance of the AI system.
    Language English
    Publishing date 2023-04-25
    Publishing country United States
    Document type Journal Article
    ISSN 2329-4302
    ISSN 2329-4302
    DOI 10.1117/1.JMI.10.5.051805
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  3. Article ; Online: Chemical Tools to Investigate Mechanisms Associated with HSP90 and HSP70 in Disease.

    Shrestha, Liza / Patel, Hardik J / Chiosis, Gabriela

    Cell chemical biology

    2016  Volume 23, Issue 1, Page(s) 158–172

    Abstract: The chaperome is a large and diverse protein machinery composed of chaperone proteins and a variety of helpers, such as the co-chaperones, folding enzymes, and scaffolding and adapter proteins. Heat shock protein 90s and 70s (HSP90s and HSP70s), the most ...

    Abstract The chaperome is a large and diverse protein machinery composed of chaperone proteins and a variety of helpers, such as the co-chaperones, folding enzymes, and scaffolding and adapter proteins. Heat shock protein 90s and 70s (HSP90s and HSP70s), the most abundant chaperome members in human cells, are also the most complex. As we have learned to appreciate, their functions are context dependent and manifested through a variety of conformations that each recruit a subset of co-chaperone, scaffolding, and folding proteins and which are further diversified by the posttranslational modifications each carry, making their study through classic genetic and biochemical techniques quite a challenge. Chemical biology tools and techniques have been developed over the years to help decipher the complexities of the HSPs and this review provides an overview of such efforts with focus on HSP90 and HSP70.
    MeSH term(s) Animals ; HSP70 Heat-Shock Proteins/analysis ; HSP70 Heat-Shock Proteins/metabolism ; HSP90 Heat-Shock Proteins/analysis ; HSP90 Heat-Shock Proteins/metabolism ; Humans ; Models, Molecular ; Molecular Diagnostic Techniques/methods ; Molecular Probe Techniques ; Molecular Probes/analysis ; Molecular Probes/metabolism
    Chemical Substances HSP70 Heat-Shock Proteins ; HSP90 Heat-Shock Proteins ; Molecular Probes
    Language English
    Publishing date 2016-01-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ISSN 2451-9456
    ISSN (online) 2451-9456
    DOI 10.1016/j.chembiol.2015.12.006
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  4. Article ; Online: Automated Endotracheal Tube Placement Check Using Semantically Embedded Deep Neural Networks.

    Brown, Matthew S / Wong, Koon-Pong / Shrestha, Liza / Wahi-Anwar, Muhammad / Daly, Morgan / Foster, George / Abtin, Fereidoun / Ruchalski, Kathleen L / Goldin, Jonathan G / Enzmann, Dieter

    Academic radiology

    2022  Volume 30, Issue 3, Page(s) 412–420

    Abstract: Rationale and objectives: To develop artificial intelligence (AI) system that assists in checking endotracheal tube (ETT) placement on chest X-rays (CXRs) and evaluate whether it can move into clinical validation as a quality improvement tool.: ... ...

    Abstract Rationale and objectives: To develop artificial intelligence (AI) system that assists in checking endotracheal tube (ETT) placement on chest X-rays (CXRs) and evaluate whether it can move into clinical validation as a quality improvement tool.
    Materials and methods: A retrospective data set including 2000 de-identified images from intensive care unit patients was split into 1488 for training and 512 for testing. AI was developed to automatically identify the ETT, trachea, and carina using semantically embedded neural networks that combine a declarative knowledge base with deep neural networks. To check the ETT tip placement, a "safe zone" was computed as the region inside the trachea and 3-7 cm above the carina. Two AI outputs were evaluated: (1) ETT overlay, (2) ETT misplacement alert messages. Clinically relevant performance metrics were compared against prespecified thresholds of >85% overlay accuracy and positive predictive value (PPV) > 30% and negative predictive value NPV > 95% for alerts to move into clinical validation.
    Results: An ETT was present in 285 of 512 test cases. The AI detected 95% (271/285) of ETTs, 233 (86%) of these with accurate tip localization. The system (correctly) did not generate an ETT overlay in 221/227 CXRs where the tube was absent for an overall overlay accuracy of 89% (454/512). The alert messages indicating that either the ETT was misplaced or not detected had a PPV of 83% (265/320) and NPV of 98% (188/192).
    Conclusion: The chest X-ray AI met prespecified performance thresholds to move into clinical validation.
    MeSH term(s) Humans ; Artificial Intelligence ; Retrospective Studies ; Intubation, Intratracheal/methods ; Trachea/diagnostic imaging ; Neural Networks, Computer
    Language English
    Publishing date 2022-05-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1355509-1
    ISSN 1878-4046 ; 1076-6332
    ISSN (online) 1878-4046
    ISSN 1076-6332
    DOI 10.1016/j.acra.2022.04.022
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  5. Article: Copper mediated coupling of 2-(piperazine)-pyrimidine iodides with aryl thiols using Cu(I)thiophene-2-carboxylate

    Shrestha, Liza / Patel, Hardik J / Kang, Yanlong / Sharma, Sahil / Chiosis, Gabriela / Taldone, Tony

    Tetrahedron letters. 2017 Nov. 29, v. 58, no. 48

    2017  

    Abstract: A copper-mediated synthesis of diaryl sulfides utilizing Cu(I)-thiophene-2-carboxylate (CuTC) is described. We demonstrate the use of CuTC as a soluble, non-basic catalyst in the coupling of aryl iodides and aryl thiols in the synthesis of synthetically ... ...

    Abstract A copper-mediated synthesis of diaryl sulfides utilizing Cu(I)-thiophene-2-carboxylate (CuTC) is described. We demonstrate the use of CuTC as a soluble, non-basic catalyst in the coupling of aryl iodides and aryl thiols in the synthesis of synthetically advanced diaryl sulfides. This method allows for the successful coupling of challenging substrates including ortho-substituted and heteroaryl iodides and thiols. Additionally, most of the aryl iodide substrates used here contain the privileged piperazine scaffold bound to a pyrimidine, pyridine, or phenyl ring and thus this method allows for the elaboration of complex piperazine scaffolds into molecules of biological interest. The method described here enables the incorporation of late-stage structural diversity into diaryl sulfides containing the piperazine ring, thus enhancing the number and nature of derivatives available for SAR investigation.
    Keywords catalysts ; chemical reactions ; chemical structure ; copper ; iodides ; piperazine ; pyridines ; sulfides ; thiols
    Language English
    Dates of publication 2017-1129
    Size p. 4525-4531.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 204287-3
    ISSN 1873-3581 ; 0040-4039
    ISSN (online) 1873-3581
    ISSN 0040-4039
    DOI 10.1016/j.tetlet.2017.10.041
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  6. Article ; Online: Heat Shock Protein (HSP) Drug Discovery and Development: Targeting Heat Shock Proteins in Disease.

    Shrestha, Liza / Bolaender, Alexander / Patel, Hardik J / Taldone, Tony

    Current topics in medicinal chemistry

    2016  Volume 16, Issue 25, Page(s) 2753–2764

    Abstract: Heat shock proteins (HSPs) present as a double edged sword. While they play an important role in maintaining protein homeostasis in a normal cell, cancer cells have evolved to co-opt HSP function to promote their own survival. As a result, HSPs such as ... ...

    Abstract Heat shock proteins (HSPs) present as a double edged sword. While they play an important role in maintaining protein homeostasis in a normal cell, cancer cells have evolved to co-opt HSP function to promote their own survival. As a result, HSPs such as HSP90 have attracted a great deal of interest as a potential anticancer target. These efforts have resulted in over 20 distinct compounds entering clinical evaluation for the treatment of cancer. However, despite the potent anticancer activity demonstrated in preclinical models, to date no HSP90 inhibitor has obtained regulatory approval. In this review we discuss the unique challenges faced in targeting HSPs that have likely contributed to their lack of progress in the clinic and suggest ways to overcome these so that the enormous potential of these compounds to benefit patients can finally be realized. We also provide a guideline for the future development of HSP-targeted agents based on the many lessons learned during the last two decades in developing HSP90 inhibitors.
    MeSH term(s) Antineoplastic Agents/pharmacology ; Drug Discovery ; Heat-Shock Proteins/antagonists & inhibitors ; Heat-Shock Proteins/metabolism ; Humans ; Protein Binding
    Chemical Substances Antineoplastic Agents ; Heat-Shock Proteins
    Language English
    Publishing date 2016-04-12
    Publishing country United Arab Emirates
    Document type Journal Article ; Review
    ZDB-ID 2064823-6
    ISSN 1873-4294 ; 1568-0266
    ISSN (online) 1873-4294
    ISSN 1568-0266
    DOI 10.2174/1568026616666160413141911
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    Zs.A 5572: Show issues Location:
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  7. Article ; Online: NECA derivatives exploit the paralog-specific properties of the site 3 side pocket of Grp94, the endoplasmic reticulum Hsp90.

    Huck, John D / Que, Nanette L S / Immormino, Robert M / Shrestha, Liza / Taldone, Tony / Chiosis, Gabriela / Gewirth, Daniel T

    The Journal of biological chemistry

    2019  Volume 294, Issue 44, Page(s) 16010–16019

    Abstract: The hsp90 chaperones govern the function of essential client proteins critical for normal cell function as well as cancer initiation and progression. Hsp90 activity is driven by ATP, which binds to the N-terminal domain and induces large conformational ... ...

    Abstract The hsp90 chaperones govern the function of essential client proteins critical for normal cell function as well as cancer initiation and progression. Hsp90 activity is driven by ATP, which binds to the N-terminal domain and induces large conformational changes that are required for client maturation. Inhibitors targeting the ATP-binding pocket of the N-terminal domain have anticancer effects, but most bind with similar affinity to cytosolic Hsp90α and Hsp90β, endoplasmic reticulum Grp94, and mitochondrial Trap1, the four cellular hsp90 paralogs. Paralog-specific inhibitors may lead to drugs with fewer side effects. The ATP-binding pockets of the four paralogs are flanked by three side pockets, termed sites 1, 2, and 3, which differ between the paralogs in their accessibility to inhibitors. Previous insights into the principles governing access to sites 1 and 2 have resulted in development of paralog-selective inhibitors targeting these sites, but the rules for selective targeting of site 3 are less clear. Earlier studies identified 5'
    MeSH term(s) Adenosine-5'-(N-ethylcarboxamide)/analogs & derivatives ; Adenosine-5'-(N-ethylcarboxamide)/pharmacology ; Allosteric Regulation ; Binding Sites ; Humans ; Membrane Glycoproteins/chemistry ; Membrane Glycoproteins/metabolism ; Molecular Docking Simulation ; Protein Binding
    Chemical Substances Membrane Glycoproteins ; endoplasmin ; Adenosine-5'-(N-ethylcarboxamide) (35920-39-9)
    Language English
    Publishing date 2019-09-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.RA119.009960
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  8. Article: Copper Mediated Coupling of 2-(Piperazine)-pyrimidine Iodides with Aryl Thiols using Cu(I)Thiophene-2-carboxylate.

    Shrestha, Liza / Patel, Hardik J / Kang, Yanlong / Sharma, Sahil / Chiosis, Gabriela / Taldone, Tony

    Tetrahedron letters

    2017  Volume 58, Issue 48, Page(s) 4525–4531

    Abstract: A copper-mediated synthesis of diaryl sulfides utilizing Cu(I)-thiophene-2-carboxylate (CuTC) is described. We demonstrate the use of CuTC as a soluble, non-basic catalyst in the coupling of aryl iodides and aryl thiols in the synthesis of synthetically ... ...

    Abstract A copper-mediated synthesis of diaryl sulfides utilizing Cu(I)-thiophene-2-carboxylate (CuTC) is described. We demonstrate the use of CuTC as a soluble, non-basic catalyst in the coupling of aryl iodides and aryl thiols in the synthesis of synthetically advanced diaryl sulfides. This method allows for the successful coupling of challenging substrates including
    Language English
    Publishing date 2017-10-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 204287-3
    ISSN 1873-3581 ; 0040-4039
    ISSN (online) 1873-3581
    ISSN 0040-4039
    DOI 10.1016/j.tetlet.2017.10.041
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  9. Article ; Online: Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation.

    Rodina, Anna / Xu, Chao / Digwal, Chander S / Joshi, Suhasini / Patel, Yogita / Santhaseela, Anand R / Bay, Sadik / Merugu, Swathi / Alam, Aftab / Yan, Pengrong / Yang, Chenghua / Roychowdhury, Tanaya / Panchal, Palak / Shrestha, Liza / Kang, Yanlong / Sharma, Sahil / Almodovar, Justina / Corben, Adriana / Alpaugh, Mary L /
    Modi, Shanu / Guzman, Monica L / Fei, Teng / Taldone, Tony / Ginsberg, Stephen D / Erdjument-Bromage, Hediye / Neubert, Thomas A / Manova-Todorova, Katia / Tsou, Meng-Fu Bryan / Young, Jason C / Wang, Tai / Chiosis, Gabriela

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 3742

    Abstract: Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) ... ...

    Abstract Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based 'omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks.
    MeSH term(s) Humans ; Protein Interaction Maps ; Proteome/metabolism ; Protein Interaction Mapping ; Neoplasms/genetics ; Acclimatization
    Chemical Substances Proteome
    Language English
    Publishing date 2023-06-23
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-39241-7
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  10. Article ; Online: From medical images to flow computations without user-generated meshes.

    Dillard, Seth I / Mousel, John A / Shrestha, Liza / Raghavan, Madhavan L / Vigmostad, Sarah C

    International journal for numerical methods in biomedical engineering

    2014  Volume 30, Issue 10, Page(s) 1057–1083

    Abstract: Biomedical flow computations in patient-specific geometries require integrating image acquisition and processing with fluid flow solvers. Typically, image-based modeling processes involve several steps, such as image segmentation, surface mesh generation, ...

    Abstract Biomedical flow computations in patient-specific geometries require integrating image acquisition and processing with fluid flow solvers. Typically, image-based modeling processes involve several steps, such as image segmentation, surface mesh generation, volumetric flow mesh generation, and finally, computational simulation. These steps are performed separately, often using separate pieces of software, and each step requires considerable expertise and investment of time on the part of the user. In this paper, an alternative framework is presented in which the entire image-based modeling process is performed on a Cartesian domain where the image is embedded within the domain as an implicit surface. Thus, the framework circumvents the need for generating surface meshes to fit complex geometries and subsequent creation of body-fitted flow meshes. Cartesian mesh pruning, local mesh refinement, and massive parallelization provide computational efficiency; the image-to-computation techniques adopted are chosen to be suitable for distributed memory architectures. The complete framework is demonstrated with flow calculations computed in two 3D image reconstructions of geometrically dissimilar intracranial aneurysms. The flow calculations are performed on multiprocessor computer architectures and are compared against calculations performed with a standard multistep route.
    MeSH term(s) Cerebral Angiography/methods ; Cerebrovascular Circulation ; Computer Simulation ; Humans ; Image Processing, Computer-Assisted/methods ; Imaging, Three-Dimensional/methods ; Intracranial Aneurysm/physiopathology ; Magnetic Resonance Angiography/methods ; Reproducibility of Results ; Software
    Language English
    Publishing date 2014-04-21
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2540968-2
    ISSN 2040-7947 ; 2040-7939
    ISSN (online) 2040-7947
    ISSN 2040-7939
    DOI 10.1002/cnm.2644
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