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Chaperone proteins as ameliorators of α-synuclein-induced synaptic pathologies: insights into Parkinson’s disease

Neural Regeneration Research 2021年第6期16卷 1198-1199页

作者： Susan M.L.Banks Audrey T.Medeiros Rui Sousa Eileen M.Lafer Jennifer R.Morgan Department of Biology Florida Southern CollegeLakelandFLUSA Neuroscience Graduate Program Brown UniversityProvidenceRIUSA Department of Biochemistry and Structural Biology and Center for Biomedical Neuroscience The University of Texas Health Science Center at San AntonioSan AntonioTXUSA The Eugene Bell Center for Regenerative Biology&Tissue Engineering Marine Biological LaboratoryWoods HoleMAUSA

α-Synuclein accumulation causes synaptic vesicle trafficking defects and may underlie neurodegenerative disorders:Neurodegenerative disorders,such as Parkinson’s disease(PD)and other synucleinopathies,impact the lives of millions of patients and their *** include PD,dementia with Lewy Bodies(DLB),multiple system atrophy,and several Alzheimer’s Disease *** are clinically characterized by intracellular inclusions called Lewy Bodies,which are rich in atypical aggregates of the protein α-*** dopaminergic neurons in the substantia nigra are particularly susceptible toα-synuclein-induced aggregation and neurodegeneration,glutamatergic neurons in other brain regions(***)are also frequently affected in PD and other synucleinopathies(Schulz-Schaeffer 2010).

关键词： cortex Alzheimer insight

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Variations in kinase and effector signaling logic in a bacterial two component signaling network

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Journal of Biological Chemistry 2025年第6期301卷 108534页

作者： Swingle, Danielle Epstein, Leah Aymon, Ramisha Isiorho, Eta A. Abzalimov, Rinat R. Favaro, Denize C. Gardner, Kevin H. Structural Biology Initiative CUNY Advanced Science Research Center New YorkNY United States PhD. Program in Biochemistry The Graduate Center – City University of New York New YorkNY United States Department of Chemistry and Biochemistry City College of New York New YorkNY United States PhD. Programs in Biochemistry Biology and Chemistry The Graduate Center – City University of New York New YorkNY United States

The general stress response (GSR) protects bacteria from a wide range of stressors. In Alphaproteobacteria, GSR activation is coordinated by HWE/HisKA2 family histidine kinases (HKs), which can exhibit noncanonical structure and function. For example, while most light-oxygen-voltage sensor-containing HKs are light-activated dimers, the Rubellimicrobium thermophilum RT-HK has inverted "dark on, light off" signaling logic with a tunable monomer/dimer equilibrium. Here, we further investigate these atypical behaviors of RT-HK and characterize its downstream signaling network. Using hydrogen-deuterium exchange mass spectrometry, we find that RT-HK uses a signal transduction mechanism similar to light-activated systems, despite its inverted logic. Mutagenesis reveals that RT-HK autophosphorylates in trans, with changes to the Jα helix linking sensor and kinase domains affecting autophosphorylation levels. Exploring downstream effects of RT-HK, we identified two GSR genetic regions, each encoding a copy of the central regulator PhyR. In vitro measurements of phosphotransfer from RT-HK to the two putative PhyRs revealed that RT-HK signals only to one and does so at an increased intensity in the dark, consistent with its reversed logic. X-ray crystal structures of both PhyRs revealed a substantial shift within the receiver domain of one, suggesting a basis for RT-HK specificity. We probed further down the pathway using nuclear magnetic resonance to determine that the single NepR homolog interacts with both unphosphorylated PhyRs, and this interaction is decoupled from activation in one PhyR. This work expands our understanding of HWE/HisKA2 family signal transduction, revealing marked variations from signaling mechanisms previously identified in other GSR networks. © 2025 The Authors

关键词： Signaling

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Single-image example-based superresolution of hyperpolarized 13C images

arXiv

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arXiv 2023年

作者： Deh, Kofi Coffee, Elizabeth Zhang, Guannan Kim, Nathaniel Miloushev, Vesselin Keshari, Kayvan R. Department of Radiology Memorial Sloan Kettering Cancer Center New York CityNY United States Department of Neurology Memorial Sloan Kettering Cancer Center New York CityNY United States Department of Physiology & Biophysics Weill Cornell Graduate School New York CityNY United States Department of Biochemistry & Structural Biology Weill Cornell Graduate School NYCNY United States Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center NYCNY United States

The transient signal available for hyperpolarized (HP) 13C imaging limits the image spatial resolution. This paper demonstrates a method of increasing spatial resolution by post-processing the HP 13C metabolic map using a corresponding anatomic image as a high-resolution example. The proposed method is tested with a Shepp-Logan digital phantom and for an MR image of a tumor in a mouse brain acquired at 3 Tesla using 13C Chemical Shift Imaging. The results are compared to the results of standard image rescaling methods using peak-signal-to-noise ratio and structural similarity index (SSIM) image quality metrics. In vivo, the method reduced blur resulting in a better match between the metabolite biodistribution and the anatomy. It is concluded that the image quality of hyperpolarized 13C MRI in vivo images can be improved with single image superresolution using the anatomic image as an example. © 2023, CC0.

关键词： Magnetic resonance imaging

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Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks 25

Graph-based information diffusion method for prioritizing fu...

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25th Pacific Symposium on Biocomputing, PSB 2020

作者： Pham, Minh Lichtarge, Olivier Integrative Molecular and Biomedical Sciences Graduate Program Department of Molecular and Human Genetics Baylor College of Medicine One Baylor Plaza HoustonTX77030 United States Departments of Molecular and Human Genetics Structural and Computational Biology and Molecular Biophysics Biochemistry and Molecular Biology and Pharmacology One Baylor Plaza HoustonTX77030 United States

Shortest path length methods are routinely used to validate whether genes of interest are functionally related to each other based on biological network information. However, the methods are computationally intensive, impeding extensive utilization of network information. In addition, nonweighted shortest path length approach, which is more frequently used, often treat all network connections equally without taking into account of confidence levels of the associations. On the other hand, graph-based information diffusion method, which employs both the presence and confidence weights of network edges, can efficiently explore large networks and has previously detected meaningful biological patterns. Therefore, in this study, we hypothesized that the graph-based information diffusion method could prioritize genes with relevant functions more efficiently and accurately than the shortest path length approaches. We demonstrated that the graph-based information diffusion method substantially differentiated not only genes participating in same biological pathways (p 0.0001) but also genes associated with specific human drug-induced clinical symptoms (p 0.0001) from random. Furthermore, the diffusion method prioritized these functionally related genes faster and more accurately than the shortest path length approaches (pathways: p = 2.7e-28, clinical symptoms: p = 0.032). These data show the graph-based information diffusion method can be routinely used for robust prioritization of functionally related genes, facilitating efficient network validation and hypothesis generation, especially for human phenotypespecific genes. © 2019 The Authors.

关键词： Genes

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Virtual Flavonoids Screening Identifies Potent Compounds Against Enterovirus A71 and Coxsackievirus A16

SSRN

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SSRN 2023年

作者： Sripattarphan, Amita Sanachai, Kamonpan Chavasiri, Warinthorn Wolschann, Peter Langer, Thierry Boonyasuppayakorn, Siwaporn Rungrotmongkol, Thanyada Center of Excellence in Structural and Computational Biology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand Department of Biochemistry Faculty of Science Khon Kaen University Khon Kaen40002 Thailand Center of Excellence in Natural Products Chemistry Department of Chemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand Department of Pharmaceutical Chemistry Faculty of Life Sciences University of Vienna Althanstraße 14 ViennaA-1090 Austria Institute of Theoretical Chemistry University of Vienna Vienna1090 Austria Center of Excellence in Applied Medical Virology Department of Microbiology Faculty of Medicine Chulalongkorn University Bangkok10330 Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok10330 Thailand

Worldwide outbreaks of hand, foot, and mouth disease (HFMD) are caused by enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16). Since no anti-HFMD drugs are currently available, it is interesting to study potential viral inhibitors. Rupintrivir is a rhinovirus 3C protease (3Cpro) inhibitor with apparent inhibitory activity against HFMD. This study constructs pharmacophore models of the EV-A71 and CV-A16 3Cpro complexed with rupintrivir using molecular dynamics (MD) simulations. Both models had similar pharmacophore features, including hydrogen bond donors and acceptors and hydrophobic interactions. These pharmacophore models were then used as a template to screen 39 flavonoid compounds as potential novel inhibitors. Diosmin, epigallocatechin gallate (EGCG), and RTH-011 showed high binding affinities for EV-A71 and CV-A16 3Cpro. They formed hydrogen bonds with important surrounding residues in both proteins, including H40, L127, T142, A144, T145, H161, I162, G163, and G164. In addition, their effective concentrations against rhabdomyosarcoma (RD) cell infection by EV-A71 and CV-A16 were determined. EGCG had the highest half maximal effective concentration (EC50) of 12.86 ± 1.30 µM for EV-A71 and 15.54 ± 1.50 µM for CV-A16, while diosmin had EC50 of 21.01±1.57 µM for EV-A71 and 30.68 ± 3.25 µM for CV-A16. Both compounds were non-toxic in RD cells, with 50% cytotoxic concentrations of >100 µM for EGCG and >500 µM for diosmin. In addition, MD simulation analysis showed that EGCG had a higher binding affinity than diosmin, supported by its significantly lower solvated binding free energies and greater numbers of contact atoms and key binding residues. Moreover, previous studies reported EGCG’s inhibitory effect on other viruses, such as severe acute respiratory syndrome coronavirus 2. Therefore, our findings suggest that EGCG can effectively inhibit the EV-A71 and CV-A16 3Cpro. © 2023, The Authors. All rights reserved.

关键词： Molecular dynamics

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Buparlisib and ponatinib inhibit aggressiveness of cholangiocarcinoma cells via suppression of IRS1-related pathway by targeting oxidative stress resistance

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Biomedicine and Pharmacotherapy 2024年 180卷 117569-117569页

作者： Kaewlert, Waleeporn Sakonsinsiri, Chadamas Lert-itthiporn, Worachart Mahalapbutr, Panupong Ali, Saba Rungrotmongkol, Thanyada Jusakul, Apinya Armartmuntree, Napat Pairojkul, Chawalit Feng, Guofei Ma, Ning Pinlaor, Somchai Murata, Mariko Thanan, Raynoo Department of Biochemistry Faculty of Medicine Khon Kaen University Khon Kaen 40002 Thailand Cholangiocarcinoma Research Institute Khon Kaen University Khon Kaen 40002 Thailand Center of Excellence in Structural and Computational Biology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Program in Bioinformatics and Computational Biology Graduated School Chulalongkorn University Bangkok 10330 Thailand The Center for Research and Development of Medical Diagnostic Laboratories Faculty of Associated Medical Sciences Khon Kaen University Khon Kaen 40002 Thailand Department of Medical Science Amnatcharoen Campus Mahidol University Amnat Charoen 37000 Thailand Department of Pathology Faculty of Medicine Khon Kaen University Khon Kaen 40002 Thailand Department of Environmental and Molecular Medicine Mie University Graduate School of Medicine Mie 514-8507 Japan Graduate School of Health Science Suzuka University of Medical Science Suzuka Mie 510-0226 Japan Department of Parasitology Faculty of Medicine Khon Kaen University Khon Kaen 40002 Thailand

Cholangiocarcinoma (CCA) is an oxidative stress-driven liver cancer with bile duct epithelial cell phenotypes and currently lacks effective treatments, making targeted drug therapy urgently needed. Oxidative stress plays a critical role in CCA carcinogenesis, involving cells with oxidative stress resistance via upregulation of the PI3K and MEKK3 signaling pathways. In this study, we investigated the antineoplastic efficacy of a PI3K inhibitor (buparlisib) and a multi-tyrosine kinase inhibitor (ponatinib) on CCA. The cytotoxicity of the drug combination was studied in vitro using CCA cell lines and in vivo using CCA xenograft models. It was found that the drug combination suppressed growth, colony formation, and migration abilities of CCA cells and induced oxidative damage, cell cycle arrest, and autophagy by suppressing MEKK3 and YAP1 through inhibition of insulin receptor substrate 1 (IRS1) signaling. Moreover, the drugs would potentially bind to the IRS1 protein, significanly decreasing IRS1 phosphorylation. Additionally, the drug combination significantly diminished the expression of YAP1, the cell proliferation marker and an antioxidant regulator, and increased oxidative stress-responsive markers in the xenograft model. In conclusion, targeting oxidative stress resistance with combined buparlisib and ponatinib suppressed tumor growth and migration by repressing IRS1-related pathways and ultimately inducing oxidative damage, suggesting the potential for targeted therapy and clinical trials in CCA patients over the use of a single drug. © 2024 The Authors

关键词： Anti-cancer Bile duct cancer Buparlisib Insulin receptor substrate 1 Ponatinib Targeted therapy

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

arXiv

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arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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structural basis and synergism of ATP and Na⁺ activation in bacterial K⁺ uptake system KtrAB

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Nature Communications 2024年第1期15卷 3850页

作者： Chiang, Wesley Tien Chang, Yao-Kai Hui, Wei-Han Chang, Shu-Wei Liao, Chen-Yi Chang, Yi-Chuan Chen, Chun-Jung Wang, Wei-Chen Lai, Chien-Chen Wang, Chun-Hsiung Luo, Siou-Ying Huang, Ya-Ping Chou, Shan-Ho Horng, Tzyy-Leng Hou, Ming-Hon Muench, Stephen P. Chen, Ren-Shiang Tsai, Ming-Daw Hu, Nien-Jen Graduate Institute of Biochemistry National Chung Hsing University Taichung 402202 Taiwan Institute of Biological Chemistry Academia Sinica Taipei 115201 Taiwan Department of Civil Engineering National Taiwan University Taipei 106319 Taiwan Department of Biomedical Engineering National Taiwan University Taipei 10663 Taiwan Life Science Group Scientific Research Division National Synchrotron Radiation Research Center Hsinchu 30092 Taiwan Institute of Molecular Biology National Chung Hsing University Taichung 402202 Taiwan Graduate Institute of Chinese Medical Science China Medical University Taichung 406040 Taiwan Department of Applied Mathematics Feng Chia University Taichung 407102 Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung 402202 Taiwan School of Biomedical Sciences Faculty of Biological Sciences and the Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT United Kingdom Department of Life Science Tunghai University Taichung 407224 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei 106319 Taiwan Ph.D Program in Translational Medicine National Chung Hsing University Taichung 402202 Taiwan

The K+ uptake system KtrAB is essential for bacterial survival in low K+ environments. The activity of KtrAB is regulated by nucleotides and Na+. Previous studies proposed a putative gating mechanism of KtrB regulated...

The K⁺ uptake system KtrAB is essential for bacterial survival in low K⁺ environments. The activity of KtrAB is regulated by nucleotides and Na⁺. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na⁺ activates KtrAB and the Na⁺ binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na⁺, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na⁺ binding stabilizes the ATP-bound BsKtrAB complex and enhances its K⁺ flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na⁺ in activating BsKtrAB is likely applicable to Na⁺-activated K⁺ channels in central nervous system. © The Author(s) 2024.

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Inhibition of topoisomerase IIα and induction of DNA damage in cholangiocarcinoma cells by altholactone and its halogenated benzoate derivatives

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Biomedicine and Pharmacotherapy 2020年 127卷 110149-110149页

作者： Kitdumrongthum, Sarunya Reabroi, Somrudee Suksen, Kanoknetr Tuchinda, Patoomratana Munyoo, Bamroong Mahalapbutr, Panupong Rungrotmongkol, Thanyada Ounjai, Puey Chairoungdua, Arthit Toxicology Graduate Program Faculty of Science Mahidol University Bangkok Thailand Excellent Center for Drug Discovery (ECDD) Mahidol University Bangkok Thailand Department of Pharmacology Faculty of Science Mahidol University Bangkok Thailand Department of Physiology Faculty of Science Mahidol University Bangkok Thailand Department of Chemistry Faculty of Science Mahidol University Bangkok Thailand Structural and Computational Biology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok Thailand Department of Biology Faculty of Science Mahidol University Bangkok Thailand

Topoisomerase IIα enzyme (Topo IIα) plays a critical function in DNA replication process and is considered to be a promising target of anti-cancer drugs. In the present study, we reported that the altholactone derivatives modified by adding a halogenated benzoate group showed greater inhibitory activity on Topo IIα enzyme in cell-free system concomitant with cytotoxicity against the CCA cell lines (KKU-M055 and KKU-M213) than those of the parent altholactone. However, the cytotoxic activities of four halogenated benzoate altholactone derivatives including iodo-, fluoro-, chloro-, and bromobenzoate derivatives (compound 1, 2, 3, and 4, respectively) were of equal potency. The fluorobenzoate derivative (compound 2) was chosen for investigating the underlying mechanism in CCA cells. Compound 2 arrested CCA cell cycle at sub G1 phase and induced apoptotic cell death. It markedly inhibited Topo IIα protein expression in both KKU-M055 and KKU-M213 cells, which was accompanied by DNA double-strand breaks demonstrated by an increase in phosphorylated H2A.X protein. Interestingly, KKU-M055 cells, which express higher Topo IIα mRNA compared to KKU-M213 cells, showed greater sensitivity to the compound, indicating the selectivity of the compound to Topo IIα enzyme. By computational docking analysis, the binding affinity of altholactone (-52.5 kcal/mol) and compound 2 (-56.7 kcal/mol) were similar to that of the Topo II poison salvicine (-53.7 kcal/mol). The aromatic moiety of both altholactones embedded in a hydrophobic pocket of Topo II ATPase domain. In addition, compound 2 induced the formation of linear DNA in Topo II-mediated cleavage assay. Collectively, our results demonstrate that the addition of fluorobenzoyl group to altholactone enhances potency and selectivity to inhibit type IIα topoisomerases. Atholactone and fluorobenzoate derivative act as Topo II cleavage complexes stabilizing compounds or Topo II poisons preferentially through binding at ATPase domain of Topo

关键词： Altholactone Cholangiocarcinoma Halogenated benzoate Topoisomerase IIα

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Front Cover: Design, Synthesis, and Characterization of Novel Styryl Dyes as Fluorescent Probes for Tau Aggregate Detectionin Vitroand in Cells (Chem. Asian J. 6/2024)

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Chemistry – An Asian Journal 2024年第6期19卷

作者： Withsakorn Sangsuwan Kriangsak Faikhruea Kotchakorn Supabowornsathit Don Sangsopon Praewphan Ingrungruanglert Hathaichanok Chuntakaruk Napatsaporn Nuntavanotayan Kittiporn Nakprasit Nipan Israsena Thanyada Rungrotmongkol Pitak Chuawong Tirayut Vilaivan Chanat Aonbangkhen Center of Excellence in Natural Products Chemistry (CENP) Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Department of Chemistry and Center of Excellence for Innovation in Chemistry Faculty of Science Special Research Unit for Advanced Magnetic Resonance (AMR) Kasetsart University Bangkok 10900 Thailand These authors are contributed equally. Organic Synthesis Research Unit Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Stem Cell and Cell Therapy Research Unit and Department of Pharmacology Faculty of Medicine Chulalongkorn University Bangkok 10330 Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok 10330 Thailand Center of Excellence in Structural and Computational Biology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand

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