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arXiv 2024年

作者： Barton, Brandon Sagal, Jacob Feeney, Sean Grattan, George Patnaik, Pratik Oganesyan, Vadim Carr, Lincoln D. Kapit, Eliot Quantum Engineering Program Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Physics Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Computer Science Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Department of Physics and Astronomy College of Staten Island City University of New York Staten IslandNY10314 United States Physics program and Initiative for the Theoretical Sciences The Graduate Center City University of New York New YorkNY10016 United States

In this work, we introduce a new iterative quantum algorithm, called Iterative Symphonic Tunneling for Satisfiability problems (IST-SAT), which solves quantum spin glass optimization problems using high-frequency oscillating transverse fields. IST-SAT operates as a sequence of iterations, in which bitstrings returned from one iteration are used to set spin-dependent phases in oscillating transverse fields in the next iteration. Over several iterations, the novel mechanism of the algorithm steers the system toward the problem ground state. We benchmark IST-SAT on sets of hard MAX-3-XORSAT problem instances with exact state vector simulation, and report polynomial speedups over trotterized adiabatic quantum computation (TAQC) and the best known semi-greedy classical algorithm. When IST-SAT is seeded with a sufficiently good initial approximation, the algorithm converges to exact solution(s) in a polynomial number of iterations. Our numerical results identify a critial Hamming radius(CHR), or quality of initial approximation, where the time-to-solution crosses from exponential to polynomial scaling in problem size. By combining IST-SAT with future classical or quantum approximation algorithms, larger gains may be achieved. The mechanism we present in this work thus presents a new path toward achieving quantum advantage in optimization. © 2024, CC BY.

关键词： Combinatorial optimization

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Discovery of dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) inhibitors using an artificial intelligence model and their effects on tau and tubulin dynamics

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Biomedicine and Pharmacotherapy 2024年 181卷 117688-117688页

作者： Chen, Jun-Hong Tu, Huang-Ju Lin, Tony Eight Peng, Zhao-Xiang Wu, Yi-Wen Yen, Shih-Chung Sung, Tzu-Ying Hsieh, Jui-Hua Lee, Hsueh-Yun Pan, Shiow-Lin HuangFu, Wei-Chun Hsu, Kai-Cheng Graduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei Taiwan Ph.D. Program for Cancer Molecular Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei Taiwan Warshel Institute for Computational Biology The Chinese University of Hong Kong Guangdong Shenzhen China Division of Translational Toxicology National Institute of Environmental Health Sciences National Institutes of Health Durham NC United States School of Pharmacy College of Pharmacy Taipei Medical University Taipei Taiwan TMU Research Center of Cancer Translational Medicine Taipei Medical University Taipei Taiwan Cancer Center Wan Fang Hospital Taipei Medical University Taipei Taiwan

The dual-specificity tyrosine-phosphorylation-regulated kinase 1 A (DYRK1A) presents a promising therapeutic target for neurological diseases. However, current inhibitors lack selectivity, which can lead to unexpected side effects and increase the difficulty of studying DYRK1A. Therefore, identifying selective inhibitors targeting DYRK1A is essential for reducing side effects and facilitating neurological disease research. This study aimed to discover DYRK1A inhibitors through a screening pipeline incorporating a deep neural network (DNN) model. Herein, we report an optimized model with an accuracy of 0.93 on a testing set. The pipeline was then performed to identify potential DYRK1A inhibitors from the National Cancer Institute (NCI) library. Four novel DYRK1A inhibitors were identified, and compounds NSC657702 and NSC31059 were noteworthy for their potent inhibition, with IC₅₀ values of 50.9 and 39.5 nM, respectively. NSC31059 exhibited exceptional selectivity across 70 kinases. The compounds also significantly reduced DYRK1A-induced tau phosphorylation at key sites associated with the pathology of neurodegenerative diseases. Moreover, they promoted tubulin polymerization, suggesting a role in microtubule stabilization. Cytotoxicity assessments further confirmed the neuronal safety of the compounds. Together, the results demonstrated a promising screening pipeline and novel DYRK1A inhibitors as candidates for further optimization and development. © 2024 The Authors

关键词： Deep Learning DYRK1A Tau

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GW190521 as a black-hole merger coincident with the ZTF19abanrhr flare

arXiv

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arXiv 2021年

作者： Bustillo, Juan Calderón Leong, Samson H.W. Chandra, Koustav McKernan, Barry Ford, K.E.S. Instituto Galego de Física de Altas Enerxías Universidade de Santiago de Compostela Galicia Santiago de Compostela15782 Spain Department of Physics The Chinese University of Hong Kong N.T. Shatin Hong Kong Department of Physics Indian Institute of Technology Bombay Powai Maharashtra Mumbai400076 India Department of Science CUNY-BMCC 199 Chambers St. New YorkNY10007 United States Department of Astrophysics American Museum of Natural History Central Park West New YorkNY10028 United States Physics Program The Graduate Center CUNY New YorkNY10016 United States Center for Computational Astrophysics Flatiron Institute New YorkNY10010 United States

We present an analysis that reconciles the gravitational wave signal GW190521 observed by the Advanced LIGO and Advanced Virgo detectors with the electromagnetic flare ZTF19abanrhr observed by the Zwicky Transient Facility. We analyze GW190521 under a mass-ratio prior uniform in Q ∈ [1, 4] using the state-of-the-art waveform model for black-hole mergers NRSur7dq4. We find a 90% credible region for the black-hole masses extending far outside what originally reported by [1], where our maximum likelihood masses reside. We find a 15% probability that both black holes avoid the pair-instability supernova gap. We infer a three-dimensional sky-location highly consistent with ZTF19abanrhr, obtaining an odds-ratio OC/R = 72: 1 that strongly favors the hypothesis of a true coincidence over a random one. Combining this event with the neutron-star merger GW170817, we estimate a Hubble constant H0 = 72.1-6.4+10.6km s-1 Mpc-1 at the 68% credible level. Copyright © 2021, The Authors. All rights reserved.

关键词： Merging

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Functional characterization of Alzheimer’s disease genetic variants in microglia

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Nature Genetics 2023年第10期55卷 1735-1744页

作者： Yang, Xiaoyu Wen, Jia Yang, Han Jones, Ian R. Zhu, Xiaodong Liu, Weifang Li, Bingkun Clelland, Claire D. Luo, Wenjie Wong, Man Ying Ren, Xingjie Cui, Xiekui Song, Michael Liu, Hongjiang Chen, Cady Eng, Nicolas Ravichandran, Mirunalini Sun, Yang Lee, David Van Buren, Eric Jiang, Min-Zhi Chan, Candace S. Y. Ye, Chun Jimmie Perera, Rushika M. Gan, Li Li, Yun Shen, Yin Institute for Human Genetics University of California San Francisco San Francisco CA United States Department of Genetics University of North Carolina Chapel Hill NC United States Pharmaceutical Sciences and Pharmacogenomics Graduate Program University of California San Francisco San Francisco CA United States Helen and Robert Appel Alzheimer’s Disease Research Institute Feil Family Brain and Mind Research Institute Weill Cornell Medicine New York City NY United States Department of Biostatistics University of North Carolina Chapel Hill NC United States Department of Neurology University of California San Francisco San Francisco CA United States Weill Institute for Neurosciences University of California San Francisco San Francisco CA United States Department of Anatomy University of California San Francisco San Francisco CA United States Division of Rheumatology Department of Medicine University of California San Francisco San Francisco CA United States Department of Biostatistics Harvard T.H. Chan School of Public Health Boston MA United States Tetrad Graduate Program University of California San Francisco San Francisco CA United States Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center University of California San Francisco San Francisco CA United States Department of Epidemiology and Biostatistics University of California San Francisco San Francisco CA United States Parker Institute for Cancer Immunotherapy San Francisco CA United States Chan Zuckerberg Biohub San Francisco CA United States Bakar Computational Health Sciences Institute University of California San Francisco San Francisco CA United States Department of Pathology University of California San Francisco San Francisco CA United States Helen Diller Family Comprehensive Cancer Center University of California San Francisco San Francisco CA United States Department of Computer Science University of North Carolina Chapel Hill NC United States

Candidate cis-regulatory elements (cCREs) in microglia demonstrate the most substantial enrichment for Alzheimer’s disease (AD) heritability compared to other brain cell types. However, whether and how these genome-wide association studies (GWAS) variants contribute to AD remain elusive. Here we prioritize 308 previously unreported AD risk variants at 181 cCREs by integrating genetic information with microglia-specific 3D epigenome annotation. We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. In addition, we show that AD variants exhibit allelic imbalance on target gene expression. In particular, rs7922621 is the effective variant in controlling TSPAN14 expression among other nominated variants in the same cCRE and exerts multiple physiological effects including reduced cell surface ADAM10 and altered soluble TREM2 (sTREM2) shedding. Our work represents a systematic approach to prioritize and characterize AD-associated variants and provides a roadmap for advancing genetic association to experimentally validated cell-type-specific phenotypes and mechanisms. © 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.

关键词： Epigenomics Functional genomics

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Is there any linkage between interstellar aldehyde and alcohol?

arXiv

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arXiv 2021年

作者： Mondal, Suman Kumar Gorai, Prasanta Sil, Milan Ghosh, Rana Etim, Emmanuel E. Chakrabarti, Sandip K. Shimonishi, Takashi Nakatani, Naoki Furuya, Kenji Tan, Jonathan C. Das, Ankan Indian Centre for Space Physics 43 Chalantika Garia Station Road Kolkata700084 India Department of Space Earth and Environment Chalmers University of Technology GothenburgSE-412 96 Sweden Department of Chemical Sciences Federal University Wukari Katsina-Ala Road P.M.B. 1020 Taraba State Wukari Nigeria Center for Transdisciplinary Research Niigata University Nishi-ku Niigata950-2181 Japan Environmental Science Program Department of Science Faculty of Science Niigata University Nishi-ku Niigata950-2181 Japan Institute for Catalysis Hokkaido University N21W10 Kita-ku Hokkaido Sapporo001-0021 Japan Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan Department of Astronomy University of Virginia CharlottesvilleVA22904 United States Department of Chemistry Graduate School of Science and Engineering Tokyo Metropolitan University 1-1 Minami-Osawa Hachioji Tokyo192-0397 Japan National Astronomical Observatory of Japan Tokyo181-8588 Japan

It is speculated that there might be some linkage between interstellar aldehydes and their corresponding alcohols. Here, an observational study and astrochemical modeling are coupled together to illustrate the connection between them. The ALMA cycle 4 data of a hot molecular core, G10.47+0.03 is utilized for this study. Various aldehydes (acetaldehyde, propanal, and glycolaldehyde), alcohols (methanol and ethylene glycol), and a ketone (acetone) are identified in this source. The excitation temperatures and the column densities of these species were derived via the rotation diagram method assuming LTE conditions. An extensive investigation is carried out to understand the formation of these species. Six pairs of aldehyde-alcohol: i) methanal and methanol;ii) ethanal and ethanol;iii) propanal and 1-propanol;iv) propenal and allyl alcohol;v) propynal and propar gyl alcohol;vi) glycolaldehyde and ethylene glycol;vii) along with one pair of ketone-alcohol (acetone and isopropanol) and viii) ketene-alcohol (ethenone and vinyl alcohol) are considered for this study. Two succes sive hydrogenation reactions in the ice phase are examined to form these alcohols from aldehydes, ketone, and ketene, respectively. Quantum chemical methods are extensively executed to review the ice phase formation route and the kinetics of these species. Based on the obtained kinetic data, astrochemical modeling is employed to derive the abundances of these aldehydes, alcohols, ketone, and ketene in this source. It is seen that our model could successfully explain the observed abundances of various species in this hot molecular core. Copyright © 2021, The Authors. All rights reserved.

关键词： Acetone

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Accuracy of a new rapid diagnostic test for urinary antigen detection and assessment of drug treatment in opisthorchiasis

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Infectious Diseases of Poverty 2023年第6期12卷 79-90页

作者： Chanika Worasith Jiraporn Sithithaworn Phattharaphon Wongphutorn Chutima Homwong Kanoknan Khongsukwiwat Anchalee Techasen Kulthida Y.Kopolrat Watcharin Loilome Nisana Namwat Bandit Thinkamrop Chaiwat Tawarungruang Attapol Titapun Thewarach Laha Ross H.Andrews Simon D.Taylor‑Robinson Paiboon Sithithaworn Department of Adult Nursing Faculty of NursingKhon Kaen UniversityKhon KaenThailand Cholangiocarcinoma Research Institute Khon Kaen UniversityKhon KaenThailand Faculty of Associated Medical Sciences Khon Kaen UniversityKhon KaenThailand Biomedical Science Program Graduate SchoolKhon Kaen UniversityKhon KaenThailand Faculty of Public Health Kasetsart University Chalermphrakiat Sakon Nakhon Province CampusSakon NakhonThailand Department of Systems Biosciences and Computational Medicine Faculty of MedicineKhon Kaen UniversityKhon KaenThailand Khon Kaen University Phenome Centre Khon Kaen UniversityKhon KaenThailand Department of Epidemiology and Biostatistics Faculty of Public HealthKhon Kaen UniversityKhon KaenThailand Department of Surgery Faculty of MedicineKhon Kaen UniversityKhon KaenThailand Depart‑ment of Parasitology Faculty of MedicineKhon Kaen UniversityKhon KaenThailand Faculty of Medicine St Mary’s CampusImperial College LondonLondonUK Division of Digestive Health Department of Surgery and Can‑cerImperial College LondonLondonUK

Background Screening for opisthorchiasis,a parasitic worm infection affecting many millions of people in Southeast Asia,has traditionally relied on faecal egg examination such as the formalin-ethyl acetate concentration technique(FECT)and Kato-Katz *** the urinary enzyme-linked immunosorbent assay(ELISA)has been used more recently,we developed a urinary antigen-based rapid diagnostic test(RDT)to simplify diagnosis and as a point-of-care testing(POCT)and field applications for surveillance and control of *** A urinaryOpisthorchis viverrini(OV)-RDT was developed using immunochromatographic methodology with a specific monoclonal antibody against *** diagnostic performance of the urinary OV-RDT was compared to that of quantitative faecal FECT and urinary antigen ELISA(n=493).Cross-reactivities of urinary OV-RDT with other helminthiases coexisted *** were determined(n=96).A field trial in the application of urinary OV-RDT was compared with urinary antigen ELISA at baseline screening and assessment of drug treatment outcomes in opisthorchiasis(n=1629).The McNemar chi-square,Kruskal-Wallis and Cohen’s kappa coefficient(κ-value)tests were used for statistical *** Urinary OV-RDT had sensitivity of 94.2%and specificity of 93.2%,compared to faecal *** OV-RDT had high diagnostic agreement(Kappa=0.842-0.874,P<0.001)and quantitative correlation with urinary antigen ELISA(Kruskal-Wallis tests=316.2,P<0.0001)and faecal FECT(Kruskal-Wallis tests=362.3,P<0.0001).The positive rates by OV-RDT,ELISA and FECT were 48.9%,52.5%and 49.3%,***-reactions of urinary OV-RDT with other helminthiases were few(2%).Field trials of urinary OV-RDT yielded comparable prevalence *** between urinary OV-RDT(53.2%)and urinary antigen ELISA(54.0%).OV screening showed high diagnostic agreement(kappa>0.8,P<0.0001)between urinary OV-RDT and urinary antigen *** cure rates of opisthorchiasis at 1 month post-praziq

关键词： Liver fluke Opisthorchis viverrini Urinary antigen detection Urinary Opisthorchis viverrini rapid diagnosis test Enzyme-linked immunosorbent assay Quantitative formalin-ethyl acetate concentration technique

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In silico identification of a novel Cdc2-like kinase 2 (CLK2) inhibitor in triple negative breast cancer

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Protein science 2024年第6期33卷 e5004-e5004页

作者： Huang, Cheng-Chiao Hsu, Chia-Ming Chao, Min-Wu Hsu, Kai-Cheng Lin, Tony Eight Yen, Shih-Chung Tu, Huang-Ju Pan, Shiow-Lin Ph.D. Program for Cancer Molecular Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University and Academia Sinica Taipei Taiwan Division of General Surgery Department of Surgery Taipei Medical University Hospital Taipei Taiwan Graduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei Taiwan School of Medicine College of Medicine National Sun Yat-sen University Kaohsiung Taiwan Institute of Biopharmaceutical Sciences College of Medicine National Sun Yat-sen University Kaohsiung Taiwan The Doctoral Program of Clinical and Experimental Medicine College of Medicine National Sun Yat-sen University Kaohsiung Taiwan Ph.D. Program in Drug Discovery and Development Industry College of Pharmacy Taipei Medical University Taipei Taiwan TMU Research Center of Cancer Translational Medicine Taipei Medical University Taipei Taiwan TMU Research Center of Drug Discovery Taipei Medical University Taipei Taiwan Warshel Institute for Computational Biology The Chinese University of Hong Kong (Shenzhen) Guangdong Shenzhen China

Dysregulation of RNA splicing processes is intricately linked to tumorigenesis in various cancers, especially breast cancer. Cdc2-like kinase 2 (CLK2), an oncogenic RNA-splicing kinase pivotal in breast cancer, plays a significant role, particularly in the context of triple-negative breast cancer (TNBC), a subtype marked by substantial medical challenges due to its low survival rates. In this study, we employed a structure-based virtual screening (SBVS) method to identify potential CLK2 inhibitors with novel chemical structures for treating TNBC. Compound 670551 emerged as a novel CLK2 inhibitor with a 50% inhibitory concentration (IC₅₀) value of 619.7 nM. Importantly, Compound 670551 exhibited high selectivity for CLK2 over other protein kinases. Functionally, this compound significantly reduced the survival and proliferation of TNBC cells. Results from a cell-based assay demonstrated that this inhibitor led to a decrease in RNA splicing proteins, such as SRSF4 and SRSF6, resulting in cell apoptosis. In summary, we identified a novel CLK2 inhibitor as a promising potential treatment for TNBC therapy. © 2024 The Authors. Protein science published by Wiley Periodicals LLC on behalf of The Protein Society.

关键词： CLK2 drug discovery kinase inhibitor structure-based virtual screening triple-negative breast cancer

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A web-based, hospital-wide health care-associated bloodstream infection surveillance and classification system: Development and evaluation

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JMIR Medical Informatics 2015年第3期3卷 e31页

作者： Tseng, Yi-Ju Wu, Jung-Hsuan Lin, Hui-Chi Chen, Ming-Yuan Ping, Xiao-Ou Sun, Chun-Chuan Shang, Rung-Ji Sheng, Wang-Huei Chen, Yee-Chun Lai, Feipei Chang, Shan-Chwen Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Computational Health Informatics Program Boston Children's Hospital Boston MA United States Department of Electrical Engineering National Taiwan University Taipei Taiwan Center for Infection Control National Taiwan University Hospital Taipei Taiwan National Taiwan University Hospital Information Systems Office Taipei Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Department of Internal Medicine National Taiwan University Hospital and College of Medicine Taipei Taiwan National Health Research Institutes National Institute of Infectious Diseases and Vaccinology Miaoli Taiwan

Background: Surveillance of health care-associated infections is an essential component of infection prevention programs, but conventional systems are labor intensive and performance dependent. Objective: To develop an automatic surveillance and classification system for health care-associated bloodstream infection (HABSI), and to evaluate its performance by comparing it with a conventional infection control personnel (ICP)-based surveillance system. Methods: We developed a Web-based system that was integrated into the medical information system of a 2200-bed teaching hospital in Taiwan. The system automatically detects and classifies HABSIs. Results: In this study, the number of computer-detected HABSIs correlated closely with the number of HABSIs detected by ICP by department (n=20;r=.999 P<.001) and by time (n=14;r=.941;P<.001). Compared with reference standards, this system performed excellently with regard to sensitivity (98.16%), specificity (99.96%), positive predictive value (95.81%), and negative predictive value (99.98%). The system enabled decreasing the delay in confirmation of HABSI cases, on average, by 29 days. Conclusions: This system provides reliable and objective HABSI data for quality indicators, improving the delay caused by a conventional surveillance system. © 2020 JMIR Publications Inc. All rights reserved.

关键词： Health care-associated infection Infection control Information systems Surveillance Web-based services

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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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Design, synthesis, and biological evaluation of indolin-2-one derivatives as novel cyclin-dependent protein kinase 8 (CDK8) inhibitors

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Biomedicine and Pharmacotherapy 2023年第1期159卷 114258-114258页

作者： Hsu, Jui-Yi Hsu, Kai-Cheng Sun, Ching Chou, Ching-Hsuan Lin, Tony Eight Sung, Tzu-Ying Tseng, Hui-Ju Yen, Shih-Chung Yang, Chia-Ron Huang, Wei-Jan Ph.D. Program for Cancer Molecular Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University and Academia Sinica Taipei Taiwan Graduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei Taiwan Ph.D. Program for Cancer Molecular Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei Taiwan Ph.D. Program in Drug Discovery and Development Industry College of Pharmacy Taipei Medical University Taipei Taiwan TMU Research Center for Drug Discovery Taipei Medical University Taipei Taiwan TMU Research Center of Cancer Translational Medicine Taipei Medical University Taipei Taiwan Cancer Center Wan Fang Hospital Taipei Medical University Taipei Taiwan School of Pharmacy College of Medicine National Taiwan University Taipei Taiwan Biomedical Translation Research Center Academia Sinica Taipei Taiwan Department of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Southern California Los Angeles CA United States Warshel Institute for Computational Biology The Chinese University of Hong Kong (Shenzhen) Guangdong Shenzhen China School of Pharmacy Taipei Medical University Taipei Taiwan

Cyclin-dependent protein kinase 8 (CDK8) plays important roles in regulating fibrotic growth factors and inflammatory signaling pathways. Long-term chronic inflammation of the lungs can lead to idiopathic pulmonary fibrosis (IPF). Abnormal alveolar epithelial regeneration leads to the release of various fibrotic growth factors and the activation of inflammatory cells. CDK8 regulates profibrotic cytokines broadly implicated in the pathogenesis of fibrosis. Therefore, inhibition of CDK8 is considered a promising strategy for treating IPF. Here, CDK8 inhibitors were designed and optimized using a fragment-based drug design strategy. Testing results revealed that 71% of the synthesized compounds inhibited CDK8 activity better than the original compound E966–0530. Of these compounds, compound 4k exhibited the strongest CDK8 enzyme-inhibiting activity (IC₅₀ =129 nM). Notably, it displayed a 13-fold increase in potency when compared to E966–0530. Experiments on toxicity and inhibition of epithelial-mesenchymal transition (EMT) protein expressions showed that compound 4k can inhibit EMT protein expressions, but with no significant cytotoxicity for alveolar epithelial cells. Compound 4k showed a potent inhibitory effect in cell migration assays. Furthermore, compound 4k significantly inhibited the phosphorylation of p-Smad3 and RNA Pol II, which are critical mediators in the fibrotic response signaling pathway. Compound 4k remarkably reduced TGF-β1-induced oxidative stress. The above results reveal optimized CDK8 inhibitors with potential use for IPF therapeutic treatment. © 2023 The Authors

关键词： Cyclin-dependent protein kinase 8 (CDK8) Idiopathic pulmonary fibrosis (IPF) Indolin-2-one Kinase inhibitor Lead optimization

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