SYNAPTA: An artificial genetic system and its application for the generation of novel nucleic acid therapeutics

生命的多样性主要基于两种聚合物的多功能性：多肽（即蛋白质）和多核苷酸（核酸）。特别是核酸显示出其编码遗传信息能力之外的独特特性，这使其成为化学、生物技术、纳米技术和医学的重要工具。核酸也具有巨大的治疗潜力，但受到DNA和RNA化学固有的系统性限制，如血清/核酸酶稳定性差。核酸适配体是一种很有前途的生物分子治疗药物，基于结构单链核酸，在某些临床环境中具有与抗体竞争的潜力。广泛的基于RNA和dna的适配体已经被描述为针对广泛的靶标，其中一些目前正在进行临床试验，强调了它们的潜力。然而，基于天然核酸（如RNA或DNA）的试剂在临床试剂和疗法的许多理想特性方面并不是最佳的，特别是体内稳定性和生物利用度。原则上，适体可以通过药物化学方法稳定（选择后），这种方法已经被Macugen验证，Macugen是第一个基于适体的药物，已被批准用于治疗黄斑变性。然而，选择后修饰可以改变和/或削弱适体结构和靶相互作用，并可能改变适体的特异性。因此，使用修饰的核酸化学直接选择是可取的。许多新的核酸结构已经建立，以增加正交性的观点。这里的挑战是设计支架，使其与细胞遗传机制的相互作用/干扰最小，同时保持与之沟通的能力。化学正交核酸的另一种方法涉及到主链的修饰，但保留信息核碱基的完整。用其他戊糖（或己糖和四糖）替代标准核糖呋喃糖确实会对螺旋构象和双相稳定性和形成产生巨大影响。我们选择了两种非天然的核酸结构，己醇核酸（HNA）和环己烯基核酸（CeNA）作为我们的主链结构。HNA和CeNA都完全抵抗核酸酶降解，似乎不是DNA或RNA修饰酶的底物。值得注意的是，它们作为核苷酸对细胞无毒，因此似乎不被细胞复制、转录和翻译机器识别为底物。该提案旨在开发所需的平台技术，以提供基于这些具有明显潜力的新型生物治疗药物的新型化学物质的高血清稳定性，定义紧凑结构和扩展功能的量身定制的“设计师”配体。这些新型聚合物还将通过研究完全基于非自然化学的人工遗传系统，为分子信息存储和传播参数提供见解。

Life's diversity is largely based on the versatility of two polymers: polyeptides (i.e. proteins) and polynucleotides (nucleic acids). Nucleic acids in particular display unique properties beyond their ability to encode genetic information, which make them important tools in chemistry, biotechnology, nanotechnology and medicine. Nucleic acids also have enormous potential as therapeutics but suffer from systemic constraints inherent in DNA and RNA chemistry such as poor serum / nuclease stability. Aptamers are a promising class of biomolecular therapeutics based on structured single-stranded nucleic acids with the potential to rival antibodies in some clinical settings. A broad spectrum of both RNA- and DNA-based aptamers have been described directed against a wide-range of targets and several are currently undergoing in clinical trails underlining their potential. However, reagents based on natural nucleic acids such as RNA or DNA are not optimal with respect to a number of desirable properties for clinical reagents and therapeutics, notably in vivo stability and bioavailability. In principle, aptamers may be stabilized (post-selection) by medicinal chemistry approaches and this approach has been validated by the Macugen, the 1st aptamers based drug, which has been approved for the treatment of macular degeneration. However, post-selection modifications can alter and / or weaken aptamer structure and target interactions and may modify aptamer specificity. Therefore direct selections using modified nucleic acid chemistries would be desirable. Many novel nucleic acid structures have been built with a view towards increased orthogonality. The challenge here is to design scaffolds that lead to minimal interaction / interference with the cellular genetic machinery while simultaneously maintaining an ability to communicate with it. A different approach towards chemically orthogonal nucleic acids involves the modification of the backbone but leaves the informational nucleobases intact. Replacement of the canonical ribofuranose with other pentoses (or hexoses and tetroses) can indeed have dramatic effects on helical conformation and duplex stability and formation. We have selected two unnatural nucleic acid architectures, Hexitol nucleic acid (HNA) and Cyclohexenyl nucleic acids (CeNA) as our backbone structures. Both HNA and CeNA are completely resistant to nuclease degradation and appear not to be substrates for DNA or RNA modifying enzymes. Significantly, they are non-toxic to cells as nucleotides and therefore appear to be not recognized as substrates by the cellular replication, transcription and translation machine. This proposal aims to develop the platform technologies needed to deliver tailor-made 'designer' ligands of high serum stability, defined compact structure and expanded functionality based on these novel chemistries with obvious potential as a novel class of bio-therapeutics. These novel polymers will also provide insights into the parameters of molecular information storage and propagation through the study of artificial genetic systems entirely based on unnatural chemistry.