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Structure-Based Pharmacophore Modeling to Discover Novel CCR5 Inhibitors for HIV-1/Cancers Therapy

Journal of Biomedical Science and Engineering 2019年第1期12卷 10-30页

作者： hsuan-Yu Lin Yih Ho hsuan-liang liu Institute of Biochemical and Biomedical Engineering National Taipei University of Technology Taiwan School of Pharmacy Taipei Medical University Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taiwan

CC chemokine receptor 5 (CCR5), a member of G protein-coupled receptors (GPCRs), not only plays a significant role in inflammatory responses, but also correlates with HIV-1 infection and cancer progression. Recently, blocking of CCR5 has been considered as an effective strategy in HIV-1/cancers therapy. So far, only Maraviroc has been approved by FDA in 2007, while the other CCR5 inhibitors have failed in their clinical trials. In this study, a highly selective structure-based pharmacophore model was constructed, validated, and applied for virtual screening to retrieve novel CCR5 inhibitors from NCI database. Finally, one potential CCR5 inhibitor candidate, NSC13165, was identified after molecular docking, molecular dynamics (MD) simulations, binding free energy analyses and ADMET prediction. Docking and MD simulation results not only suggested that NSC13165 reserves the common binding mode of the most known CCR5 inhibitors, but also provided important insights toward the allosteric inhibition mechanism of CCR5. The results of binding free energy analyses indicated that the binding affinity of NSC13165 is much better than that of Maraviroc and that van der Waals interaction is the key driving force during the binding process. ADMET prediction suggested that NSC13165 exhibits very low risk of causing lethal side effects. Altogether, our results strongly suggest that NSC13165 has great potential to serve as a novel CCR5 inhibitor, which may be further tested in vitro/in vivo as a drug target for HIV-1/cancers therapy or be used as a lead compound for improving its efficacy through chemical modifications.

关键词： CCR5 Inhibitor HIV-1 Maraviroc Virtual Screening Molecular Dynamics Simulation

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Discovery of Novel Irreversible HER2 Inhibitors for Breast Cancer Treatment

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Journal of Biomedical Science and Engineering 2019年第4期12卷 225-244页

作者： Jhih-Yan Tang Yih Ho Chun-Yi Chang hsuan-liang liu Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taiwan School of Pharmacy College of Pharmacy Taipei Medical University Taiwan Institute of Biochemical and Biomedical Engineering National Taipei University of Technology Taiwan

It has been widely known that human epidermal growth factor receptor 2 (HER2) inhibitors exhibit distinct antitumor responses against HER2-positive breast cancer. To date, Lapatinib (Tykerb®) has been approved by the U.S. Food and Drug Administration (FDA) as a reversible HER2 inhibitor for treating breast cancer. However, HER2 L755S, T798I and T798M mutations confer drug resistance to lapatinib, restricting its efficacy toward HER2-positive breast cancer. Thus, novel therapy toward mutant HER2 is highly desired. Although several irreversible HER2 inhibitors have been developed to overcome these drug resistance problems, most of them were reported to cause severe side effects. In this study, three pharmacophore models based on HER2 L755S, T798I and T798M mutant structures were constructed and then validated through receiver operating characteristic (ROC) curve analysis and Güner-Henry (GH) scoring methods. Subsequently, these well-validated models were utilized as 3D queries to identify novel irreversible HER2 inhibitors from National Cancer Institute (NCI) database. Finally, two potential irreversible HER2 inhibitor candidates, NSC278329 and NSC718305, were identified and validated through molecular docking, molecular dynamics (MD) simulations and ADMET prediction. Furthermore, the analyses of binding modes showed that both NSC278329 and NSC718305 exhibit good binding interactions with HER2 L755S, T798I and T798M mutants. All together, the above results suggest that both NSC278329 and NSC718305 can serve as novel and effective irreversible HER2 inhibitors for treating breast cancers with HER2 L755S, T798I and T798M mutants. In addition, they may act as lead compounds for designing new irreversible HER2 inhibitors by carrying out structural modifications and optimizations in future studies.

关键词： Breast Cancer Irreversible HER2 Inhibitors Structure-Based Pharmacophore Modeling Molecular Docking Mo-lecular Dynamics Simulation

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Discovery of Novel N-Glycoside and Non-Glycoside hSGLT2 Inhibitors for the Treatment of Type 2 Diabetes Mellitus

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Journal of Diabetes Mellitus 2019年第3期9卷 77-104页

作者： Chun-Yi Chang Yih Ho Shwu-Jiuan Lin hsuan-liang liu Institute of Biochemical and Biomedical Engineering National Taipei University of Technology Taiwan School of Pharmacy Taipei Medical University Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taiwan

Human sodium-glucose cotransporter 2 (hSGLT2) is a membrane protein responsible for glucose reabsorption from the glomerular filtrate in the proximal tubule. Inhibition of hSGLT2 has been regarded as a brand new therapeutic approach for the treatment of type 2 diabetes mellitus (T2DM) due to its non-insulin related characteristics with less side effects. Current commercially available hSGLT2 inhibitors are all C-glycoside inhibitors. Previous studies have reported that N-glycoside inhibitors have better potential to serve as new drugs due to their good metabolic stability. In addition, non-glycoside inhibitors have been shown to exhibit the capability to overcome the existing problems of current glycoside inhibitors, including low tissue permeability, poor stability and short serum half-time. Here, we aimed to discover novel N-glycoside and non-glycoside hSGLT2 inhibitors by a combination of several computational approaches. A ligand-based pharmacophore model was generated, well validated and subsequently utilized as a 3D query to identify novel hSGLT2 inhibitors from National Cancer Institute (NCI) and Traditional Chinese Medicine (TCM) databases. Finally, one N-glycoside (NSC679207) and one non-glycoside (TCM_Piperenol_A) hSGLT2 inhibitors were successfully identified, which were proven to exhibit excellent binding affinities, pharmacokinetic properties and less toxicity than the commercially available hSGLT2 inhibitor, canagliflozin, via molecular docking, ADMET prediction, molecular dynamics (MD) simulations and binding free energy calculations. All together, our results strongly suggest that these two compounds have great potential to serve as novel hSGLT2 inhibitors for the treatment of T2DM and their efficacies may be further examined by a series of in vitro and/or in vivo bioassays.

关键词： Human Sodium-Glucose Cotransports 2 (hSGLT2) Type 2 Diabetes Mellitus (T2DM) Ligand-Based Pharmacophore Model Molecular Docking Molecular Dynamics (MD) Simulations

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Identification of Novel CDK9 Inhibitors with Better Inhibitory Activity and Higher Selectivity for Cancer Treatment by an Effective Two-Stage Virtual Screening Strategy

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Journal of Biomedical Science and Engineering 2021年第12期14卷 371-390页

作者： Szu-Hung Chen Yu-Ru Wang Yih Ho Shu-Juan Lin hsuan-liang liu Institute of Biochemical and Biomedical Engineering National Taipei University of Technology Taiwan School of Pharmacy College of Pharmacy Taipei Medical University Taiwan Department of Chemical Engineering & Biotechnology National Taipei University of Technology Taiwan

The aberrant overexpression of cyclin-dependent kinase 9 (CDK9) in cancer cells results in the loss of proliferative control, making it an attractive therapeutic target for various cancers. However, the highly structural similarity between CDK9 and CDK2 makes the development of novel selective CDK9 inhibitors a challenging task and thus limits their clinical applications. Here, an effective two-stage virtual screening strategy was developed to identify novel CDK9 inhibitors with better inhibitory activity and higher selectivity. The first screening stage aims to select potential compounds with better inhibitory activity than Roniciclib, one of the most effective CDK9 inhibitors, through reliable structure-based pharmacophoric virtual screening and accurate molecular docking analyses. The second stage employs a very detailed visual inspection process, in which several structural criteria describing the major difference between the binding pockets of CDK9 and CDK2 are taken into consideration, to identify compounds with higher selectivity than CAN508, one of the CDK9 inhibitors with distinguished selectivity. Finally, three compounds (NCI207113 from NCI database and TCM0004 and TCM3282 from TCM database) with better inhibitory activity and higher selectivity were successfully identified as novel CDK9 inhibitors. These three compounds also display excellent binding stabilities, great pharmacokinetic properties and low toxicity in MD simulations and ADMET predictions. Besides, the results of binding free energy calculations suggest that enhancing van der Waals interaction and nonpolar solvation energy and/or reducing polar solvation energy can significantly improve the binding affinity of these CDK9 inhibitors. Their clinical potentials to serve as anticancer drug candidates can be further evaluated through a series of in vitro/in vivo bioassays in the future. To the best of our knowledge, this is the first attempt to identify novel CDK9 inhibitors with both be

关键词： Cyclin-Dependent Kinase 9 (CDK9) Structure Based Pharmacophore Modeling Virtual Screening

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Optimization Strategies of Na_(3)V_(2)(PO_(4))_(3) Cathode Materials for Sodium‑Ion Batteries

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Nano-Micro Letters 2025年第2期17卷 204-251页

作者： Jiawen Hu Xinwei Li Qianqian liang Li Xu Changsheng Ding Yu liu Yanfeng Gao School of Materials Science and Engineering Shanghai UniversityShanghai 200444People’s Republic of China Shanghai Institute of Ceramics Chinese Academy of SciencesShanghai 200050People’s Republic of China

Na_(3)V_(2)(PO_(4))_(3)(NVP)has garnered great attentions as a prospective cathode material for sodium-ion batteries(SIBs)by virtue of its decent theoretical capacity,superior ion conductivity and high structural ***,the inherently poor electronic conductivity and sluggish sodium-ion diffusion kinetics of NVP material give rise to inferior rate performance and unsatisfactory energy density,which strictly confine its further application in ***,it is of significance to boost the sodium storage performance of NVP cathode *** to now,many methods have been developed to optimize the electrochemical performance of NVP cathode *** this review,the latest advances in optimization strategies for improving the electrochemical performance of NVP cathode material are well summarized and discussed,including carbon coating or modification,foreign-ion doping or substitution and nanostructure and morphology *** foreign-ion doping or substitution is highlighted,involving Na,V,and PO_(4)^(3−)sites,which include single-site doping,multiple-site doping,single-ion doping,multiple-ion doping and so ***,the challenges and prospects of high-performance NVP cathode material are also put *** is believed that this review can provide a useful reference for designing and developing high-performance NVP cathode material toward the large-scale application in SIBs.

关键词： Sodium-ion batteries Na_(3)V_(2)(PO_(4))_(3) Cathode materials Electrochemical performance Optimization strategies

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Flexible Graphene Field‑Effect Transistors and Their Application in Flexible Biomedical Sensing

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Nano-Micro Letters 2025年第2期17卷 252-313页

作者： Mingyuan Sun Shuai Wang Yanbo liang Chao Wang Yunhong Zhang Hong liu Yu Zhang Lin Han Institute of Marine Science and Technology Shandong UniversityQingdao 266237ShandongPeople’s Republic of China State Key Laboratory of Crystal Materials Shandong UniversityJinan 250100ShandongPeople’s Republic of China School of Integrated Circuits Shandong UniversityJinan 250100ShandongPeople’s Republic of China Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application Jinan250100ShandongPeople’s Republic of China

Flexible electronics are transforming our lives by making daily activities more *** to this innovation are field-effect transistors(FETs),valued for their efficient signal processing,nanoscale fabrication,low-power consumption,fast response times,and ***,known for its exceptional mechanical properties,high electron mobility,and biocompatibility,is an ideal material for FET channels and *** combination of graphene and FETs has given rise to flexible graphene field-effect transistors(FGFETs),driving significant advances in flexible electronics and sparked a strong interest in flexible biomedical ***,we first provide a brief overview of the basic structure,operating mechanism,and evaluation parameters of FGFETs,and delve into their material selection and patterning *** ability of FGFETs to sense strains and biomolecular charges opens up diverse application *** specifically analyze the latest strategies for integrating FGFETs into wearable and implantable flexible biomedical sensors,focusing on the key aspects of constructing high-quality flexible biomedical ***,we discuss the current challenges and prospects of FGFETs and their applications in biomedical *** review will provide valuable insights and inspiration for ongoing research to improve the quality of FGFETs and broaden their application prospects in flexible biomedical sensing.

关键词： Flexible Graphene Field-effect transistor Wearable Implantable Biosensor

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Human neural stem cell-derived extracellular vesicles protect against ischemic stroke by activating the PI3K/AKT/mTOR pathway

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Neural Regeneration Research 2025年第11期20卷 3245-3258页

作者： Jiayi Wang Mengke Zhao Dong Fu Meina Wang Chao Han Zhongyue Lv liang Wang Jing liu Stem Cell Clinical Research Center The First Affiliated Hospital of Dalian Medical UniversityDalianLiaoning ProvinceChina Dalian Innovation Institute of Stem Cell and Precision Medicine DalianLiaoning ProvinceChina Institute(College)of Integrative Medicine Dalian Medical UniversityDalianLiaoning ProvinceChina

Human neural stem cell-derived extracellular vesicles exhibit analogous functions to their parental cells,and can thus be used as substitutes for stem cells in stem cell therapy,thereby mitigating the risks of stem cell therapy and advancing the frontiers of stem cell-derived *** lays a foundation for the development of potentially potent new treatment modalities for ischemic ***,the precise mechanisms underlying the efficacy and safety of human neural stem cell-derived extracellular vesicles remain unclear,presenting challenges for clinical *** promote the translation of therapy based on human neural stem cell-derived extracellular vesicles from the bench to the bedside,we conducted a comprehensive preclinical study to evaluate the efficacy and safety of human neural stem cell-derived extracellular vesicles in the treatment of ischemic *** found that administration of human neural stem cell-derived extracellular vesicles to an ischemic stroke rat model reduced the volume of cerebral infarction and promoted functional recovery by alleviating neuronal *** human neural stem cell-derived extracellular vesicles reduced neuronal apoptosis by enhancing phosphorylation of phosphoinositide 3-kinase,mammalian target of rapamycin,and protein kinase B,and these effects were reversed by treatment with a phosphoinositide 3-kinase *** findings suggest that human neural stem cell-derived extracellular vesicles play a neuroprotective role in ischemic stroke through activation of phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin signaling ***,we showed that human neural stem cell-derived extracellular vesicles have a good in vivo safety ***,human neural stem cell-derived extracellular vesicles are a promising potential agent for the treatment of ischemic stroke.

关键词： behavior exosome extracellular vesicles ischemic stroke mammalian target of rapamycin(mTOR) middle cerebral artery occlusion neural stem cells neuronal apoptosis phosphoinositide 3-kinase(PI3K) protein kinase B(AKT)

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FUBP3 mediates the amyloid-β-induced neuronal NLRP3 expression

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Neural Regeneration Research 2025年第7期20卷 2068-2083页

作者： Jing Yao Yuan Li Xi liu Wenping liang Yu Li Liyong Wu Zhe Wang Weihong Song The National Clinical Research Center for Geriatric Disease Xuanwu HospitalCapital Medical UniversityBeijingChina Department of Neurology The First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan ProvinceChina Department of Neurosurgery Xuanwu HospitalCapital Medical UniversityBeijingChina Department of Pediatrics The Second Affiliated Hospital and Yuying Children’s HospitalKey Laboratory of Alzheimer’s Disease of Zhejiang ProvinceInstitute of AgingWenzhou Medical UniversityWenzhouZhejiang ProvinceChina Oujiang Laboratory(Zhejiang Laboratory for Regenerative Medicine Visionand Brain Health)WenzhouZhejiang ProvinceChina

Alzheimer's disease is characterized by deposition of amyloid-β,which forms extracellular neuritic plaques,and accumulation of hyperphosphorylated tau,which aggregates to form intraneuronal neurofibrillary tangles,in the *** NLRP3 inflammasome may play a role in the transition from amyloid-βdeposition to tau phosphorylation and *** NLRP3 is primarily found in brain microglia,and tau is predominantly located in neurons,it has been suggested that NLRP3 expressed by microglia indirectly triggers tau phosphorylation by upregulating the expression of pro-inflammatory ***,we found that neurons also express NLRP3 in vitro and in vivo,and that neuronal NLRP3 regulates tau *** biochemical methods,we mapped the minimal NLRP3 promoter and identified FUBP3 as a transcription factor regulating NLRP3 expression in *** primary neurons and the neuroblastoma cell line Neuro2A,FUBP3 is required for endogenous NLRP3 expression and tau phosphorylation only when amyloid-βis *** the brains of aged wild-type mice and a mouse model of Alzheimer's disease,FUBP3 expression was markedly increased in cortical *** analysis suggested that FUBP3 plays a role in neuron-mediated immune *** also found that FUBP3 trimmed the 5′end of DNA fragments that it bound,implying that FUBP3 functions in stress-induced *** findings suggest that neuronal NLRP3 may be more directly involved in the amyloid-β-to–phospho-tau transition than microglial NLRP3,and that amyloid-βfundamentally alters the regulatory mechanism of NLRP3 expression in *** that FUBP3 was only expressed at low levels in young wild-type mice and was strongly upregulated in the brains of aged mice and Alzheimer's disease mice,FUBP3 could be a safe therapeutic target for preventing Alzheimer's disease progression.

关键词： 5′end trimming Alzheimer's disease amyloid-beta amyloid-β-dependent transcription FUBP3 inflammasome inflammation neuron NLRP3 tau transcription factor

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A promising approach for quantifying focal stroke modeling and assessing stroke progression:optical resolution photoacoustic microscopy photothrombosis

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Neural Regeneration Research 2025年第7期20卷 2029-2037页

作者： Xiao liang Xingping Quan Xiaorui Geng Yujing Huang Yonghua Zhao Lei Xi Zhen Yuan Ping Wang Bin liu Faculty of Health Sciences University of MacaoMacao Special Administrative RegionChina Center for Cognitive and Brain Sciences University of MacaoMacao Special Administrative RegionChina Department of Biomedical Engineering Southern University of Science and TechnologyShenzhenGuangdong ProvinceChina State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical SciencesUniversity of MacaoTaipaMacao Special Administrative RegionChina Department of Emergency Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdong ProvinceChina

To investigate the mechanisms underlying the onset and progression of ischemic stroke,some methods have been proposed that can simultaneously monitor and create embolisms in the animal cerebral ***,these methods often require complex systems and the effect of age on cerebral embolism has not been adequately studied,although ischemic stroke is strongly *** this study,we propose an optical-resolution photoacoustic microscopy-based visualized photothrombosis methodology to create and monitor ischemic stroke in mice simultaneously using a 532 nm pulsed *** observed the molding process in mice of different ages and presented age-dependent vascular embolism ***,we integrated optical coherence tomography angiography to investigate age-associated trends in cerebrovascular variability following a *** imaging data and quantitative analyses underscore the differential cerebrovascular responses to stroke in mice of different ages,thereby highlighting the technique's potential for evaluating cerebrovascular health and unraveling age-related mechanisms involved in ischemic strokes.

关键词： age-dependent cerebral cortex ischemic stroke mouse model optical coherence tomography angiography photoacoustic microscopy photothrombosis vascular imaging

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MXene Hybridized Polymer with Enhanced Electromagnetic Energy Harvest for Sensitized Microwave Actuation and Self-Powered Motion Sensing

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NANO-MICRO LETTERS 2025年第1期17卷 1-15页

作者： Wang, Yu-Ze Wang, Yu-Chang liu, Ting-Ting Zhao, Quan-liang Li, Chen-Sha Cao, Mao-Sheng Beijing Inst Technol Sch Mat Sci & Engn Beijing 100081 Peoples R China Peking Univ Sch Mat Sci & Engn Beijing 100871 Peoples R China North China Univ Technol Sch Mech & Mat Engn Beijing 100144 Peoples R China Heilongjiang Univ Minist Educ Peoples Republ China Key Lab Funct Inorgan Mat Chem Harbin 150080 Peoples R China

Polymeric microwave actuators combining tissue-like softness with programmable microwave-responsive deformation hold great promise for mobile intelligent devices and bionic soft robots. However, their application is challenged by restricted electromagnetic sensitivity and intricate sensing coupling. In this study, a sensitized polymeric microwave actuator is fabricated by hybridizing a liquid crystal polymer with Ti3C2Tx (MXene). Compared to the initial counterpart, the hybrid polymer exhibits unique space-charge polarization and interfacial polarization, resulting in significant improvements of 230% in the dielectric loss factor and 830% in the apparent efficiency of electromagnetic energy harvest. The sensitized microwave actuation demonstrates as the shortened response time of nearly 10 s, which is merely 13% of that for the initial shape memory polymer. Moreover, the ultra-low content of MXene (up to 0.15 wt%) benefits for maintaining the actuation potential of the hybrid polymer. An innovative self-powered sensing prototype that combines driving and piezoelectric polymers is developed, which generates real-time electric potential feedback (open-circuit potential of similar to 3 mV) during actuation. The polarization-dominant energy conversion mechanism observed in the MXene-polymer hybrid structure furnishes a new approach for developing efficient electromagnetic dissipative structures and shows potential for advancing polymeric electromagnetic intelligent devices.

关键词： Microwave absorption Electromagnetic response Energy harvest Self-sensing Soft actuator

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