Molecular design modelling and rationalisation of mode of action of synthetic retinoids in cellular development processes.

细胞发育过程中合成类维生素A作用模式的分子设计建模和合理化。

• 批准号: BB/G017700/1
• 金额: $ 9.48万
• 依托单位: Durham University
• 依托单位国家: 英国
• 项目类别: Training Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG017700%2F1
• 关键词: Molecular; design; modelling; rationalisation; mode

Stem cell biology has potential to provide cells and tissues of specific types for use in research, the development of pharmaceuticals and cell replacement therapies. Engineering specific tissue types from stem cells is dependent on being able to direct cell differentiation in a repeatable manner and are stable. All trans-retinoic acid (ATRA) is used to induce cell differentiation in vitro, however, it degrades resulting in products that can effect differentiation in ways not intended. To improve the efficiency of cell differentiation control, we have produced and tested a number of synthetic retinoids which have significantly improved chemical and physical stability. These compounds effect developmental change in human pluripotent stem cells and neuroblastoma cells, and like their natural counterparts, they induce a number of effects, including the formation of mature cells types, including neurons, and cell apoptosis. We have begun to build up a body of results, the first examples of which are in press, and we now need to be able to understand structure versus biological effect in order to design the next generations of more-specific small molecules. Of particular importance is the ability to design compounds which do not just act as analogues of either ATRA or the other RA isomers, but which are benign in terms of the building blocks used and do not elicit toxic effects if used for future tissue-regeneration applications. We propose to carry out molecular modelling studies to examine structure-activity relationships of synthetic retinoids compared to natural systems. Sufficient biological data are available, based on over 30 synthetic structures and 3 natural RA compounds. The competitive binding properties of many of these compounds to nuclear receptors are known, with further compounds being evaluated regularly. This provides the data required for a CASE project which will develop a molecular-level understanding of the mode of action of each of the synthetic compounds, from which new series of compounds will be designed. ATRA is a relatively flexible ligand which binds with high affinity to all RARs. Similarly, the relative flexibility of 9-cis-RA allows it to bind to RXRs as well as to RARs which results in low specificity of receptor targeting in therapeutic applications, giving side effects that limit the therapeutic potential of existing retinoids. Synthetic ligands can be designed to be conformationally rigid, allowing considerable scope for targeting specific RARs with higher specificity. The structure of RARs, particularly the ligand binding pocket of RARgamma and its interactions with a range of natural and synthetic ligands, has been elucidated at high resolution. These data permit the ligand-binding domains of RARalpha and RARbeta and their interactions with RARalpha and RARbeta-specific agonists to be modelled, facilitating the design of novel compounds with subtype specificity. This would be achieved by modelling the interactions between the ligands and the binding domain of different RARs, particularly with respect to the conformation of the carboxy-terminal helix 12 which caps the binding pocket on the receptor and the conformation of which is essential for co-activator/co-repressor recruitment and dissociation. The project will involve: a) all compounds will be modelled using molecular mechanics, molecular dynamics, DFT and/or MP2 calculations, and compared with each other, and experimental structures determined by single-crystal X-ray diffraction; b) each structure will subjected to virtual binding studies with RAR and RXR systems, to obtain an approximate rank order of estimated binding capability; c) these data will be compared with actual SAR screening data to look for correlations between virtual and actual binding. Second generation systems will be designed for further synthesis and screening.

干细胞生物学有潜力为研究、药物开发和细胞替代疗法提供特定类型的细胞和组织。从干细胞中工程化特定的组织类型依赖于能够以可重复的方式指导细胞分化并且是稳定的。所有反式维甲酸（ATRA）都被用于体外诱导细胞分化，然而，它会降解，导致产品以意想不到的方式影响分化。为了提高细胞分化控制的效率，我们已经生产和测试了许多合成类维生素a，这些类维生素a的化学和物理稳定性都得到了显著提高。这些化合物影响人类多能干细胞和神经母细胞瘤细胞的发育变化，并且像它们的天然对生物一样，它们诱导许多效应，包括成熟细胞类型的形成，包括神经元和细胞凋亡。我们已经开始建立一个结果的主体，其中的第一个例子正在出版，我们现在需要能够理解结构与生物效应，以便设计下一代更具体的小分子。特别重要的是设计化合物的能力，这些化合物不仅可以作为ATRA或其他RA异构体的类似物，而且就所使用的构建块而言是良性的，并且如果用于未来的组织再生应用，不会引起毒性作用。我们建议进行分子模拟研究，以检验合成类维生素a与天然系统的结构-活性关系。基于30多种合成结构和3种天然RA化合物，已有足够的生物学数据。许多这些化合物与核受体的竞争性结合特性是已知的，进一步的化合物正在定期评估。这为CASE项目提供了所需的数据，该项目将在分子水平上了解每种合成化合物的作用方式，并以此为基础设计新的化合物系列。ATRA是一种相对灵活的配体，对所有RARs都具有高亲和力。同样，9-顺式ra的相对灵活性使其能够与rxr和RARs结合，这导致治疗应用中受体靶向的特异性较低，产生的副作用限制了现有类维生素a的治疗潜力。合成配体可以被设计成构象刚性的，从而允许以更高的特异性靶向特定RARs的相当大的范围。RARs的结构，特别是RARgamma的配体结合袋及其与一系列天然和合成配体的相互作用，已经在高分辨率上得到了阐明。这些数据使得rarα和rarβ的配体结合结构域及其与rarα和rarβ特异性激动剂的相互作用得以建模，从而促进了具有亚型特异性的新化合物的设计。这将通过模拟配体和不同RARs结合域之间的相互作用来实现，特别是关于羧基末端螺旋12的构象，它覆盖了受体的结合囊，它的构象对于共激活物/共抑制物的募集和解离是必不可少的。该项目将涉及：a)所有化合物将使用分子力学、分子动力学、DFT和/或MP2计算进行建模，并相互比较，并通过单晶x射线衍射确定实验结构；b)每个结构将与RAR和RXR系统进行虚拟结合研究，以获得估计结合能力的大致等级顺序；c)将这些数据与实际的SAR筛选数据进行比较，寻找虚拟绑定与实际绑定之间的相关性。第二代系统将用于进一步的合成和筛选。