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.

总结 尽管在过去十年中，抗疟药物发现渠道有所改善， 许多新的候选药物可能在临床试验中失败，这是由于药物的快速出现， 抗药性寄生虫这项研究的长期目标是设计更好的临床前候选药物， 疟疾和了解为什么治疗可能失败。在过去的十年里，我们的调查小组 建立了发现和表征多药耐药基因的可靠方法， 已经收集了大量的基因和等位基因数据集，这些基因和等位基因介导或与多药耐药性相关。 此应用程序的总体目标是扩展和利用这些数据来确定何时、如何以及为什么 出现抗疟药物耐药性或持久性。我们的中心假设是，临床 可以使用体外进化分析来预测耐药性。我们还指出，阻力参数可能 暴露于现代一线药物和其他选择性药物的当前田间分离株之间存在显著差异 压力，与几十年前分离的参考实验室菌株相比。我们的假设将被验证 实现三个具体目标。在目标1中，我们将使用适应性实验室进化和深度全基因组 测序以获得耐药性获得的高分辨率视图。为了实现这一点，我们将定义 寄生虫的遗传背景在多大程度上发挥作用，通过比较最近非洲，亚洲和非洲的结果， 南美临床分离株与用可追溯到>40年前的实验室菌株获得的分离株。我们还将 测试这些菌株是否在突变途径、耐药性水平和耐药时间上有根本性差异， 最小接种量的阻力和影响的阻力寄生虫健身。我们还将回答关键问题， 关于耐药倾向是否更多地是靶标或化学型的函数的问题， 有助于抗性出现，例如基因组复制事件的数量和不同的 等位基因以及不同的化学化学型是否与给定的药物靶标相互作用产生不同的结果。在 目标2，我们将寻求了解机制的阻力在一个小组的了解甚少的调解人。这些 研究将结合联合收割机条件调控的遗传学、蛋白质组学、细胞学和结构学方法来研究 赋予寄生虫生物学抗性的遗传变化的影响。在目标3中，我们将探讨 P.恶性疟原虫基因在介导药物耐受性方面发挥作用，作为在抗疟原虫压力下生存的一种手段。创新 包括表征地理上不同的现代田间分离物中的抗性进化， 完全依靠历史上的实验室菌株。新奇包括评估耐药风险是否由 通过靶点或化学型，并确定耐受性在抗疟暴露中的作用。这 研究是重要的，因为它将改变候选药物的选择方式， 临床和临床前研究，最好是在早期先导阶段。