Drug Repurposing Screening for Rare and Neglected Diseases

罕见病和被忽视疾病的药物再利用筛查

• 批准号: 10910751
• 负责人: Wei Zheng
• 金额: $ 285.93万
• 依托单位: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10910751
• 关键词: 2019-nCoV; ABCB1 gene; Acceleration; Action Potentials; Affect; Alagille Syndrome; Animal Model; Area; Artificial Intelligence; Axon; BAY 54-9085; Biological Assay; Biotechnology; Brain; COVID-19; COVID-19 screening; CREB1 gene; Cardiac Myocytes; Cell Differentiation process; Cell Line; Cells; Cessation of life; Clinical; Clinical Data; Clinical Treatment; Clinical Trials; Collaborations; Collection; Computer Models; Data; Deposition; Development; Disease; Disease model; Doxorubicin; Drug Costs; Drug Industry; Drug Screening; Drug Targeting; Drug resistance; Drug usage; Estrogen Receptors; Eye diseases; FOXG1B gene; Foundations; Generations; Genes; Genetic; Genetic Diseases; Goals; Hepatocyte; Hereditary Disease; Heterozygote; Human; Impaired cognition; Impairment; In Vitro; Incidence; Industry; Intellectual functioning disability; Laboratories; Lead; Leber' s amaurosis; Length; Libraries; Liver; MEKs; Malignant Epithelial Cell; Malignant Neoplasms; Malignant neoplasm of liver; Malignant neoplasm of ovary; Manuscripts; Mediating; Midbrain structure; Modeling; Motor Neurons; Mucopolysaccharidosis II; Mutation; National Center for Advancing Translational Sciences; Neurodevelopmental Disorder; Neuromuscular Junction; Neurons; Neuropathy; Nonprofit Organizations; Nucleocapsid Proteins; Oncology; Organoids; Pathogenesis; Patients; Pharmaceutical Preparations; Phenotype; Photoreceptors; Positioning Attribute; Preparation; Primary carcinoma of the liver cells; Process; Publishing; Replication-Associated Process; Reporter; Research Personnel; Reserpine; Resources; Retina; SARS-CoV-2 entry inhibitor; SARS-CoV-2 infection; SARS-CoV-2 spike protein; Sampling; Screening procedure; Shrimp; Study models; Syndrome; System; TMPRSS2 gene; Terfenadine; Testing; Therapeutic; Therapeutics for Rare and Neglected Diseases; Time; Training; United States National Institutes of Health; Universities; Virus Replication; Vision; Western Blotting; Work; anticancer activity; artificial intelligence method; assay development; calmodulin-dependent protein kinase II; cancer cell; cancer drug resistance; cell repository; cell type; chemotherapy; ciliopathy; computerized; cost; detection assay; disease mechanisms study; disease phenotype; dopaminergic neuron; drug development; drug discovery; drug repurposing; drug standard; early childhood; effective therapy; experimental study; forkhead protein; high throughput screening; hypertension treatment; in vitro Assay; induced pluripotent stem cell; induced pluripotent stem cell technology; inhibitor; laboratory experiment; nanobodies; neglect; nerve stem cell; neuron development; new technology; novel strategies; novel therapeutics; particle; pre-clinical; preclinical development; rare genetic disorder; refractory cancer; screening; standard care; stem cells; therapeutic candidate; therapeutic evaluation; virtual; virtual screening

In collaboration with NIH and external academic and industry researchers, we have carried out assay development and performed drug repurposing screens for multiple projects across a range of therapeutic areas, including COVID-19, rare genetic disorders and rare drug resistant cancers. DISEASE MODELING USING PATIENT IPSC-DERIVED CELLS: Disease modeling using patient cells is an effective approach to enable establishment of new alternative / non-animal disease models. Human induced pluripotent stem cells (iPSCs) are generated from patient samples that can be further differentiated to various cell types such as neuronal cells, cardiomyocytes, and hepatocytes for disease modeling. These cell-based models are particularly useful for drug discovery and development for rare genetic diseases, as animal models are not always available. The patient derived iPSCs share the same genetic background with patients and have the same cellular disease phenotypes that are suitable for assay development to screen compounds. We have generated over 100 patient-derived iPSC lines for rare genetic diseases. In this period, we generated several iPSC lines from samples of Alagille Syndrome and healthy donors (Owusu-Ansah K et al., 2023. Stem Cell Res 71, 103135. PMID: 37393720). The iPSCs have been characterized and stably passaged over 10 passages. These iPSCs were differentiated to support generation of hepatocytes and liver organoids for ALGS disease modeling and assay development for repurposing screens. We have also deposited 6 patient iPSC lines previously generated, including for Mucopolysarcharidosis type I (MPS I) and Hunters syndrome (MPS II), to the Coriell Cell Repository as public resources to other researchers. DRUG-RESISTANT CANCER: Cancer drug resistance is a severe clinical problem that often results in patient death. We performed drug repurposing screens for drug-resistant cell lines of liver cancer, and ovarian cancer refractory to multiple standard care chemotherapies. Several approved drugs have been identified that either suppress the drug-resistant cancer cells directly or re-sensitize the cells to the anticancer activities of the standard drugs. We found that terfenadine re-sensitized doxorubicin activity in drug-resistant ovarian cancer cells via inhibition of CaMKII/CREB1-mediated ABCB1 expression (Huang W et al., 2022. Front Oncology 12, 1068443. PMID: 36439493). We also found that PD1938306, a MEK inhibitor, enhances the efficacy of sorafenib (a standard therapeutic for liver cancer) in hepatocellular carcinoma cells through a repurposing screen (Hong J eta al. 2023. Comb Chem High Throughput Screen. 26: 1364-74. PMID: 36043792). These results are useful for further studies of the mechanisms of drug resistance and cancer target identification for new drug development. SARS-CoV-2 and COVID-19: We have developed a SARS-CoV-2 pseudotyped particle entry assay for use in BSL-2 laboratories to screen compound libraries and evaluate compound efficacy as SARS-CoV-2 entry inhibitors (Xu M et al. 2022. SLAS Discovery. 27:86-94. PMID: 35086793). We have also developed a homogenous compound screening assay that detects the nucleocapsid protein of SARS-CoV-2 in the viral replication process for high throughput screening in our collaborators BSL-3 lab (Gorshkov K et al. 2022. ACS Pharmacol Transl Sci 5, 8-19. PMID: 35036857). We performed repurposing screens using the pseudotyped particle assay and another assay to target the fusion process of SARS-CoV-2 infection (Park SB et al. 2022. mBio. e0323821. PMID: 35012356). Additionally, we collaborated with other NIH researchers on COVID-19 screens related to a nanobody against the SARS-CoV-2 spike protein, TMPRSS2 inhibitors, heparan-spike interaction, and estrogen receptor-spike interaction (Fu Y et al. 2022. PLoS One. 17: e0272364. PMID: 35947606; Shrimp JH. Et al. 2022. ACS Infect Dis. 8:1191-03. PMID: 35648838; Zhang Q. et al. 2022. Sci Rep. 12:6294. PMID: 35440680; Solis O et al. 2022. Sci Adv 8, eadd4150. PMID: 36449624). FOXG1 SYNDROME: FOXG1 Syndrome is a rare and debilitating neurodevelopmental disorder causing severe cognitive impairment. The disease is caused by heterozygous mutations in the transcription factor Forkhead Box G1 (FOXG1). Currently, there is no approved therapy for FOXG1 Syndrome. BELIEVE IN A CURE is a non-profit organization focused on developing treatments for FOXG1 syndrome. NCATS collaborated with the foundation to perform a drug repurposing screen in a FOXG1 reporter assay to identify up-regulators of the FOXG1 gene. Hits from the primary screen were further tested in a Western blot assay in patient iPSC-derived neural stem cells. NGLY1 DEFICIENCY: This is a low incidence genetic disease that primarily affects the neuronal system, resulting in neuromotor impairment, intellectual disability, and neuropathy. We have generated brain organoids using the NGLY1 patient iPSCs for disease modeling. We found that the patient midbrain organoids show altered neuronal development and reduced dopaminergic neurons compared to wild type organoids (Abbott J. et al. 2023. Front Cell Dev Biol. 11: 1039182. PMID: 36875753). We also worked on a neuromuscular junction platform using the patient iPSC-derived motor neurons to study the pathogenesis of disease. We observed reduced axon length, increased and shortened axon branches, motor neuron action potential bursting, and decreased action potential firing rate and amplitude in this system (Sasserath T. et al. 2022. Adv Ther 5:2200009, PMID: 36589922). The NGLY1 brain organoids and motor neurons are useful models for the study of disease mechanisms and evaluation of therapeutic candidates. LEBER CONGENITAL AMAUROSIS (LCA): LCA is an inherited disease of the eye that causes loss of sight in early childhood and lacks effective treatment. We performed a drug repurposing screen using retinal organoids differentiated from the iPSCs from a model of Leber congenital amaurosis. Reserpine, a drug used for the treatment of hypertension, was identified among a few other compounds that maintains photoreceptor survival in retinal ciliopathy (Chen HY. Et al. 2023. Elife, 12:e83205. PMID: 36975211). Currently, further study of the mechanism of action and potential preclinical development are in process. AI-BASED MODELING AND VIRTUAL SCREENING: Recent advancements in artificial intelligence (AI)- based modeling have enabled virtual compound screening for lead compound identification. The advantages of this approach for drug discovery are (1) a reduction in physical compound screening experiments that significantly decreases project costs; and (2) a significantly increased screening capacity, as virtual screens can cover in-house compound collections as well as large commercial collections (i.e., millions of compounds), both of which save time during the lead identification process. We have developed and optimized several AI-based compound screening tools that have been applied to several projects. The experimental screening data from a small compound collection (such as the collection of 2800 approved drugs available at NCATS) is typically used to establish, train, and optimize a computer model for a given project that is then employed in a virtual compound screen of larger compound collections (up to millions of compounds) to identify hits. After computerized hit selection and confirmation, the top list compounds (typically 50 to 200) are selected and ordered for a laboratory experiment to evaluate their activities. We have published the method of AI-based modeling and virtual screening using the SARS-CoV-2 entry inhibitor project as an example (Gao P et al., 2023. J Chem Inf Model. 62: 1988-97. PMID: 35404596) with several other manuscripts under preparation.

通过与NIH以及外部学术和行业研究人员合作，我们对跨各种治疗领域的多个项目进行了测定开发，并为包括COVID-19，罕见遗传疾病和罕见的耐药性癌症的多个项目进行了药物重新利用屏幕。 使用患者IPSC衍生细胞进行疾病建模：使用患者细胞进行疾病建模是一种有效的方法，可以建立新的替代 /非动物疾病模型。人类诱导的多能干细胞（IPSC）是由患者样品产生的，可以进一步与各种细胞类型（如神经元细胞，心肌细胞和肝细胞）进行疾病模型的分化。这些基于细胞的模型对于稀有遗传疾病的药物发现和发育特别有用，因为动物模型并非总是可用。该患者衍生的IPSC与患者具有相同的遗传背景，并且具有适合于筛选化合物测定开发的相同细胞疾病表型。我们已经为罕见的遗传疾病生成了100多种患者衍生的IPSC系。在此期间，我们从阿拉吉尔综合征和健康供体样本中生成了几条IPSC线（Owusu-Ansah K等，2023。StemCell Res 71，103135。PMID：37393720）。 IPSC的表征和稳定传递了10个段落。这些IPSC被区分以支持肝细胞和肝癌的产生，以用于ALGS疾病建模和分析开发，以重新利用筛选。我们还将以前生成的6个患者IPSC系列存入了Coriell细胞存储库作为公共资源，包括I型（MPS I）和猎人综合症（MPS II）（MPS II）（MPS II）（MPS II）。 抗药性癌症：癌症耐药性是一个严重的临床问题，通常导致患者死亡。我们为肝癌的耐药细胞系和卵巢癌难治性进行了药物重新利用筛查，以对多种标准护理化疗。已经确定了几种批准的药物，可以直接抑制耐药性癌细胞，或者将细胞重新敏感到标准药物的抗癌活性。我们发现，特富纳丁通过抑制CAMKII/CREB1介导的ABCB1表达在药物耐药性卵巢癌细胞中重新敏化的阿霉素活性（Huang W等，2022。前肿瘤学12，1068443。pmid：36439493）。 我们还发现，MEK抑制剂PD1938306通过重新使用筛查增强了索拉非尼（一种标准的肝癌治疗）在肝细胞癌细胞中的功效（Hong J etaal。2023。CombChem High Tote。这些结果可用于进一步研究新药开发的耐药性和癌症靶标识别机制。 SARS-COV-2和COVID-19：我们已经开发了一种SARS-COV-2伪分型粒子进入测定法，用于在BSL-2实验室中使用，以筛选复合库并评估复合功效，作为SARS-COV-2进入抑制剂（Xu M等人2022。我们还开发了一种同质化合物筛选测定法，该测定法在我们的合作者BSL-3实验室（Gorshkov K等，2022。ACSPharmacol Transs Sci 5，8-19。PMID：350336857）中检测出高吞吐量筛选的病毒复制过程中SARS-COV-2的核蛋白蛋白。我们使用伪型粒子测定法进行了重新利用筛选，并针对SARS-COV-2感染的融合过程进行了另一种测定（Park SB等，2022。MBIO。MBIO。E0323821。PMID：35012356）。此外，我们与其他NIH研究人员在COVID-19的筛查中合作，与针对SARS-COV-2尖峰蛋白，TMPRSS2抑制剂，乙酰肝素尖峰相互作用和雌激素受体尖峰相互作用相关的纳米病毒有关（Fu Y etal。2022。 2022. FOXG1综合征：FOXG1综合征是一种罕见且令人衰弱的神经发育障碍，导致严重的认知障碍。该疾病是由转录因子Forkhead Box G1（FOXG1）中的杂合突变引起的。目前，尚无FOXG1综合征的批准疗法。相信治愈方法是一个非营利组织，专注于开发FOXG1综合征的治疗方法。 NCATS与基金会合作，在FOXG1记者测定法中进行药物重新利用屏幕，以识别FOXG1基因的上调剂。在患者IPSC衍生的神经干细胞中，在蛋白质印迹测定中进一步测试了主要筛查的命中。 NGLY1缺乏症：这是一种主要影响神经元系统的发病率低的遗传疾病，导致神经运动障碍，智力障碍和神经病。我们使用NGLY1患者IPSC进行了疾病建模生成脑器官。我们发现，与野生型类器官相比，患者中脑类器官显示出改变的神经元发育和多巴胺能神经元的降低（Abbott J.等，2023。FrontCell DevBiol。11：1039182。PMID：368775753）。我们还使用患者IPSC衍生的运动神经元研究了神经肌肉连接平台，以研究疾病的发病机理。我们观察到轴突长度减小，轴突分支增加和缩短，运动神经元动作电势爆发以及该系统的动作电势发射速率和振幅降低（Sasserath T.等，2022。DAVDTHER 5：2200009，PMID：365899922）。 NGLY1脑器官和运动神经元是研究疾病机制和评估治疗候选物的有用模型。 Leber先天性Amaurosis（LCA）：LCA是一种遗传性的眼睛疾病，可在幼儿期间导致视力丧失，缺乏有效的治疗。我们使用与Leber先天性木术模型从IPSC区分开的视网膜器官进行了一个药物重新利用的筛查。在其他几种在视网膜纤毛病中维持感光受体存活的其他化合物中，鉴定了一种用于治疗高血压的药物（Chen Hy.等，2023。Elife，12：E83205。PMID：36975211）。当前，进一步研究了作用机理和潜在的临床前发展。 基于AI的建模和虚拟筛选：基于人工智能（AI）的最新进步（基于AI）的建模已启用铅复合识别的虚拟化合物筛选。这种药物发现方法的优点是（1）降低物理化合物筛查实验，从而大大降低了项目成本； （2）筛选能力大大提高，因为虚拟屏幕可以涵盖内部化合物集合以及大型商业集合（即数百万化合物），这两者都节省了铅识别过程中的时间。我们已经开发并优化了几种基于AI的化合物筛选工具，这些工具已应用于多个项目。通常使用来自小型化合物集合的实验筛选数据（例如NCATS可用的2800名批准药物的收集），通常用于建立，训练和优化给定项目的计算机模型，然后在较大的化合物集合（多达数百万种化合物）的虚拟化合物屏幕中使用，以识别打击。在计算机命中选择和确认后，选择了最高列表化合物（通常为50至200），并订购进行实验室实验以评估其活动的。我们以SARS-COV-2条目抑制剂项目为例（Gao P等，2023。JChem Inf Model.62：1988-97。PMID：35404596），使用SARS-COV-2输入抑制剂项目进行了基于AI的建模和虚拟筛选方法。

项目成果

Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2.

• DOI: 10.3389/fphar.2020.592737
• 发表时间: 2020
• 期刊: Frontiers in pharmacology
• 影响因子: 5.6
• 作者: Chen CZ;Shinn P;Itkin Z;Eastman RT;Bostwick R;Rasmussen L;Huang R;Shen M;Hu X;Wilson KM;Brooks BM;Guo H;Zhao T;Klump-Thomas C;Simeonov A;Michael SG;Lo DC;Hall MD;Zheng W
• 通讯作者: Zheng W

Generation of an induced pluripotent stem cell line (TRNDi003-A) from a Noonan syndrome with multiple lentigines (NSML) patient carrying a p.Q510P mutation in the PTPN11 gene.

• DOI: 10.1016/j.scr.2018.101374
• 发表时间: 2019-01
• 期刊: Stem cell research
• 影响因子: 1.2
• 作者: Rong Li;Amanda Baskfield;Yongshun Lin;J. Beers;J. Zou;Chengyu Liu;F. Jaffré;A. Roberts;E. Ottinger;M. Kontaridis;Wei Zheng

Identification of novel anti-hepatitis C virus agents by a quantitative high throughput screen in a cell-based infection assay.

• DOI: 10.1016/j.antiviral.2015.10.018
• 发表时间: 2015-12
• 期刊: Antiviral research
• 影响因子: 7.6
• 作者: Hu Z;Hu X;He S;Yim HJ;Xiao J;Swaroop M;Tanega C;Zhang YQ;Yi G;Kao CC;Marugan J;Ferrer M;Zheng W;Southall N;Liang TJ
• 通讯作者: Liang TJ

Neural stem cells for disease modeling of Wolman disease and evaluation of therapeutics.

• DOI: 10.1186/s13023-017-0670-9
• 发表时间: 2017-06-28
• 期刊: Orphanet journal of rare diseases
• 影响因子: 3.7
• 作者: Aguisanda F;Yeh CD;Chen CZ;Li R;Beers J;Zou J;Thorne N;Zheng W
• 通讯作者: Zheng W

Reserpine maintains photoreceptor survival in retinal ciliopathy by resolving proteostasis imbalance and ciliogenesis defects.

• DOI: 10.7554/elife.83205
• 发表时间: 2023-03-28
• 期刊: eLife
• 影响因子: 7.7
• 作者: Chen HY;Swaroop M;Papal S;Mondal AK;Song HB;Campello L;Tawa GJ;Regent F;Shimada H;Nagashima K;de Val N;Jacobson SG;Zheng W;Swaroop A
• 通讯作者: Swaroop A