Finding an informed approach to oligonucleotide ligand screening to enable antiviral materials

第一部分：非技术摘要：作为各种生物靶点的生物启发配体，适体与抗体相比具有关键的有希望的优势，包括其低免疫原性，无动物生成，可逆变性和更长的保质期。此外，虽然在治疗性抗体开发和制造方面的研究和金融投资已经明显超过了适体的研究和金融投资，但寡核苷酸配体仍然具有作为有利的靶向甚至抑制剂的有希望的潜力，用于挑战病毒靶标，其快速传播和突变能力不幸地超过了传统的治疗发展。在缺乏先验规则来鉴定非核苷酸靶标的自杂交寡核苷酸内的潜在结合基序的情况下，找到特定靶标的正确适体（或适体组）是一个令人生畏的搜索问题，很像在国际象棋或围棋游戏中找到正确的移动，这主要是因为候选序列空间大得惊人。因此，在没有任何化学指南的情况下，研究人员传统上选择通过在称为SELEX（指数富集配体系统进化）的资源密集型筛选过程中采用由随机DNA或RNA序列成员的大异质群体（~109或更多）组成的筛选文库来简单地最大化候选适体之间的序列多样性。在这里，所提出的工作的目标是开发刺突蛋白的候选DNA适体的管道。为了实现这个雄心勃勃的目标，我们将开创一个综合的实验和信息学方法，以快速，可靠地识别DNA寡核苷酸配体从知情的，设计师库的病毒蛋白质靶点称为刺突蛋白。第二部分：技术摘要：在治疗性抗体开发和制造方面的研究和金融投资显然使鲜为人知的基于阿托西肽的配体（称为适体）黯然失色。另一方面，适体作为有利的靶向剂甚至抑制剂具有很好的潜力，用于挑战病毒靶标，其快速传播和突变能力不幸地超过了传统的治疗发展。在缺乏设计规则的情况下，为特定靶标找到正确的适体（或适体组）是一个令人生畏的搜索问题，就像在国际象棋或围棋游戏中找到正确的步骤一样，主要是因为候选序列空间大得惊人。因此，在没有任何化学指导方针的情况下，研究人员传统上选择简单地最大化筛选文库的大小（约109个或更多不同的序列），这是一种资源密集型的进化筛选过程，称为SELEX（指数富集配体的系统进化）。为了克服这种流行的适体筛选平台固有的这些具有挑战性的技术和科学瓶颈，我们建议开创一种综合的实验和信息学方法，以快速可靠地从设计师文库中识别称为刺突蛋白的病毒蛋白靶点的DNA寡核苷酸配体。所提出的集成实验/计算适体发现方法是有意地可适应的，使用“经验教训”方法来为病毒靶标铺平适体发现途径，特别是当病毒株容易突变时。这项工作将提供独特的，多学科的学生培训机会，在实验和计算方面的工作。如果成功的话，PI相信这个试点项目将为未来加速生物启发配体的发现奠定基础，以实现材料系统的理想生物活性。这个奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

PART 1: Nontechnical Abstract:As bio-inspired ligands for various biological targets, aptamers present key promising advantages over antibodies including their low immunogenicity, animal-free generation, reversible denaturation, and longer shelf-life. Moreover, while research and financial investments in therapeutic antibody development and manufacturing have clearly overshadowed that of aptamers, oligonucleotide ligands still hold promising potential as advantageous targeting and even inhibition agents for challenging viral targets whose rapid spread and mutation capabilities can unfortunately outpace traditional therapeutic developments. In the absence of a priori rules to identify potential binding motifs within a self-hybridized oligonucleotide for a non-nucleotide target, finding the right aptamer (or set of aptamers) for a particular target is a daunting search problem, much like finding the right move in a game of Chess or Go, largely because the candidate sequence space is staggeringly large. Thus, in the absence of any chemical guidelines, researchers traditionally choose instead to simply maximize the sequence diversity among candidate aptamers by employing screening libraries consisting of large heterogeneous populations (~109 or more) of random DNA or RNA sequence members in a resource-intensive screening process called SELEX (Systematic Evolution of Ligands by EXponential Enrichment). Here, the goal of the proposed work is to develop a pipeline of candidate DNA aptamers for spike protein. To undertake this ambitious goal for this pilot project we will pioneer an integrated experimental and informatics approach to rapidly and reliably identify DNA oligonucleotide ligands from informed, designer libraries for a viral protein target called the spike protein. PART 2: Technical Abstract:Research and financial investments in therapeutic antibody development and manufacturing have clearly overshadowed that of lesser known, oligonucleotide-based ligands called aptamers. Aptamers, on the other hand, hold promising potential as advantageous targeting and even inhibition agents for challenging viral targets whose rapid spread and mutation capabilities can unfortunately outpace traditional therapeutic developments. In the absence of design rules, finding the right aptamer (or set of aptamers) for a particular target is a daunting search problem, much like finding the right move in a game of Chess or Go, largely because the candidate sequence space is staggeringly large. Thus, in the absence of any chemical guidelines, researchers traditionally choose instead to simply maximize the size (~109 or more different sequences) of screening libraries in a resource-intensive, evolutionary screening process called SELEX (Systematic Evolution of Ligands by EXponential Enrichment). To overcome these challenging technical and scientific bottlenecks inherent to this popular aptamer screening platform, we propose to pioneer an integrated experimental and informatics approach to rapidly and reliably identify DNA oligonucleotide ligands from designer libraries for a viral protein target called the spike protein. The proposed integrated experimental/computational aptamer discovery approach is intentionally adaptable using a “lessons-learned” approach to pave the aptamer discovery pathway for viral targets, particularly as viral strains readily mutate. This work will offer unique, multidisciplinary student training opportunities in the experimental and computational aspects of the work. If successful the PIs believe this pilot project will lay the fundamental groundwork for future accelerated bio-inspired ligand discovery to enable desirable bioactivity of materials systems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.