Defining the resistome in P. falciparum: evolution and mechanism

恶性疟原虫抗性组的定义：进化和机制

• 批准号: 10608899
• 负责人: Daniel E. Goldberg
• 金额: $ 108.39万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-11-02 至 2027-10-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10608899
• 关键词: Address; African American; Alleles; Anti-malarial drug resistance; Antimalarials; Asian Americans; Back; Biological Assay; Biology; Biotin; Chemicals; Clinical; Clinical Research; Clinical Trials; Cryoelectron Microscopy; Data; Data Set; Development; Disease; Drug Costs; Drug Targeting; Drug Tolerance; Drug resistance; Effectiveness; Equation; Event; Evolution; Exposure to; GPT gene; Gene Mutation; Genes; Genetic; Genome; Geography; Goals; In Vitro; Infectious Agent; Knowledge; Label; Laboratories; Lead; Machine Learning; Malaria; Mediating; Mediator; Methodology; Methods; Modernization; Multi-Drug Resistance; Mutation; Parasite resistance; Parasites; Pharmaceutical Preparations; Plasmodium falciparum; Play; Probability; Proteins; Proteomics; Reproducibility; Research; Resistance; Resolution; Risk; Role; Series; South American; Structure; Testing; Time; acquired drug resistance; assay development; bioinformatics pipeline; candidate selection; candidate validation; clinically relevant; conditional knockout; cost; design; drug candidate; drug development; drug discovery; drug resistance development; effective therapy; experimental study; fitness; fungus; gene product; genome sequencing; improved; in vitro Assay; innovation; knock-down; large datasets; novel; novel therapeutics; pathogen; pathogenic bacteria; pre-clinical; preclinical development; preclinical study; predictive modeling; pressure; protein function; resistance allele; resistance gene; resistance mechanism; resistance mutation; resistant Plasmodium falciparum; small molecule inhibitor; success; trafficking; whole genome

SUMMARY Although improvements have been made to the antimalarial drug discovery pipeline over the past decade a substantial risk remains that many new drug candidates may fail in clinical trials due to the rapid emergence of drug resistant parasites. The longterm goal of this research is to design better preclinical drug candidates for both malaria and to understand why treatments may fail. Over the past decade, our investigative team has established robust methodologies for discovering and characterizing genes involved in multidrug resistance and has assembled a large dataset of genes and alleles that mediate or are associated with multidrug resistance. The overall objective of this application is to extend and leverage these data to determine when, how and why antimalarial drug resistance or persistence emerges. Our central hypothesis is that the emergence of clinical drug resistance can be predicted using in vitro evolution assays. We also posit that resistance parameters may differ substantially between current field isolates exposed to modern first-line drugs and other selective pressures, as compared with reference laboratory strains isolated decades ago. Our hypotheses will be tested by pursuing three specific aims. In Aim 1, we will use adaptive laboratory evolution and deep whole-genome sequencing to obtain a high-resolution view of drug resistance acquisition. To accomplish this, we will define the extent to which a parasite’s genetic background plays a role by comparing results from recent African, Asian and South American clinical isolates to those obtained with laboratory strains dating back >40 years. We will also test whether these strains differ fundamentally in their mutational paths, levels of and time to resistance, the minimum inoculum of resistance and the impact of resistance on parasite fitness. We will also answer the critical question of whether resistance liabilities are more a function of the target or of the chemotype, parameters that contribute to resistance emergence such as number of genome replication events and the number of different alleles and whether different chemical chemotypes interacting with a given drug target give different results. In Aim 2, we will seek to understand mechanisms of resistance in a panel of poorly understood mediators. These studies will combine conditionally regulated genetic, proteomic, cellular and structural approaches to studying the impact of genetic changes conferring resistance on parasite biology. In Aim 3, we will explore the role that P. falciparum genes play in mediating drug tolerance as a means to survive antiplasmodial pressure. Innovation includes characterizing the evolution of resistance in geographically distinct modern field isolates instead of relying entirely on historical laboratory strains. Novelty includes assessing whether the resistance risk is driven by the target or the chemotype,and defining the role for tolerance in surviving antimalarial exposure. This research is significant because it will alter the way in which drug candidates are selected prior to extensive clinical and preclinical studies, ideally at the early lead stage.

概括 尽管在过去的十年中，对抗疟药发现管道进行了改进 仍然存在很大的风险，由于临床试验的许多新候选人可能因迅速出现而失败 抗药性寄生虫。这项研究的长期目标是设计更好的临床前药物候选者 疟疾和了解为什么治疗可能失败。在过去的十年中，我们的调查团队有 建立的强大方法，用于发现和表征与多药抗性有关的基因和 已经组装了大型基因和等位基因的数据集，这些数据集介导或与多药电阻相关。 该应用程序的总体目的是扩展和利用这些数据来确定何时，如何以及为什么 抗疟疾耐药性或持久性出现。我们的中心假设是临床的出现 可以使用体外进化测定法预测耐药性。我们还肯定的是，电阻参数可能 当前暴露于现代一线药物和其他选择性的当前现场隔离株之间的基本不同 与几十年前孤立的参考实验室应变相比，压力。我们的假设将进行检验 通过追求三个具体目标。在AIM 1中，我们将使用自适应实验室进化和深层全基因组 测序以获得耐药性采集的高分辨率视图。为此，我们将定义 寄生虫的遗传背景通过比较最近的非洲，亚洲和 南美临床分离株与可追溯到40年的实验室菌株获得的临床分离株。我们也会 测试这些菌株在其突变路径，抵抗的水平和时间上是否有不同 耐药性的最低接种物和抗性对寄生虫适应性的影响。我们还将回答关键 电阻负债是否更多是目标或化学型的函数的问题，即参数 有助于抗药性出现，例如基因组复制事件的数量和不同的数量 等位基因以及不同的化学化学型与给定药物靶标相互作用是否会产生不同的结果。在 AIM 2，我们将寻求理解一组不良理解的调解人小组中的抵抗机制。这些 研究将结合有条件调节的遗传，蛋白质组学，细胞和结构方法的研究 遗传变化会议抗性对寄生虫生物学的影响。在AIM 3中，我们将探讨 恶性疟原虫基因在介导药物耐受性中发挥作用，以此作为生存的抗血状压力。创新 包括表征在地理上不同的现代野外隔离株中抗性的演变，而不是 完全依靠历史实验室菌株。新颖性包括评估阻力风险是否为驱动 通过目标或化学型，并定义了耐受性在生存抗疟疾暴露中的作用。这 研究很重要，因为它将改变在广泛之前选择候选药物的方式 临床和临床前研究，理想情况下在早期铅阶段。