Development of fragment-based approaches to build chemical tools for biology

开发基于片段的方法来构建生物学化学工具

• 批准号: BB/D006104/1
• 负责人: Chris Abell
• 金额: $ 27.6万
• 依托单位: University of Cambridge
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2006
• 资助国家: 英国
• 起止时间: 2006 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FD006104%2F1
• 关键词: Development; fragment; based; approaches; build

Enzymes catalyse chemical reactions within living cells, very quickly and very precisely. One way to cure (or kill) an organism is to slow down or stop an enzyme by using a small molecule called an enzyme inhibitor. Enzyme inhibitors have to be very selective (so they only affect the target enzyme) and they have to bind very tightly to that enzyme, so that they are not pushed off by the enzyme's normal substrate. By understanding how to inhibit an enzyme we can often learn something about how the enzyme works. The design and synthesis of enzyme inhibitors is also central to the pharmaceutical industry. Many medicines are enzyme inhibitors e.g. penicillin, pills for high blood pressure etc. So it is not surprising that ways to discover new enzyme inhibitors are very important. In the last ten years the main approach industry has used to find new enzyme inhibitors is to test millions of compounds very quickly to see if promising compounds can be found. These are then modified to be more potent and have the properties they need to be a medicine. However there is now growing interest in a completely different approach to discovering enzyme inhibitors. This involves finding a quite small molecule (called a fragment) that binds to the enzyme, and then using this as an anchor point to build up bigger more potent inhibitors. These 'fragment-based' approaches depend on methods of finding fragments. There are several ways to this, and we propose to use a number of these, some of which are well established and others which are more novel. The methods use techniques including NMR spectroscopy, mass spectrometry, and calorimetry. All rely on some way of showing the fragment binds to the enzyme, with the exception of virtual screening, where computational approaches are used to try and identify fragments that look like they should bind to the enzyme. Once we have identified fragments that bind to our target enzymes we will try and grow them into bigger molecules. One general way to do this is to mix a lot of fragments and let them react with each other in every possible combination (called dynamic combinatorial chemistry), and let the enzyme select out the one that binds to it most efficiently. It may be that the enzyme acts as a template to bring together two fragments that bind to it separately. If a lot of enzyme is used, it may lead to more of the key compound that binds to it being formed, allowing this compound to be identified as the major product. A more elegant way to identify the best binding compound, which uses less of the valuable enzyme, is to form the mixture of compounds in the presence of a crystal of the enzyme. If a compound binds to the enzyme, its identity can be deduced by solving the crystal structure of the enzyme with the molecule bound to it. We will devlop these ideas by trying to make inhibitors of two enzymes involved in making vitamin B5 (pantothenate). There is evidence to suggest that inhibitors of these enzymes may be useful against tuberculosis. Another reason to target these enzymes is that they bind molecules called NADPH and ATP, which are also used by other enzymes, so we might learn some useful general information about how to inhibit these other enzymes.

酶催化活细胞内的化学反应，非常迅速和非常精确。治愈（或杀死）有机体的一种方法是通过使用一种称为酶抑制剂的小分子来减缓或停止酶。酶抑制剂必须是非常有选择性的（所以它们只影响目标酶），它们必须与该酶非常紧密地结合，这样它们就不会被酶的正常底物推开。通过了解如何抑制一种酶，我们通常可以了解酶是如何工作的。酶抑制剂的设计和合成也是制药工业的核心。许多药物是酶抑制剂，例如青霉素，高血压药丸等，因此发现新的酶抑制剂的方法非常重要也就不足为奇了。在过去的十年里，工业界用来寻找新的酶抑制剂的主要方法是快速测试数百万种化合物，看看是否能找到有希望的化合物，然后将这些化合物改造成更有效的，并具有成为药物所需的特性。然而，现在人们对发现酶抑制剂的完全不同的方法越来越感兴趣。这涉及到找到一个相当小的分子（称为片段），结合到酶，然后使用它作为一个锚点，建立更大更有效的抑制剂。这些“基于片段”的方法依赖于寻找片段的方法。有几种方法可以做到这一点，我们建议使用其中的一些方法，其中一些方法已经很好地建立起来，而另一些方法则更新颖。这些方法使用的技术包括NMR光谱法、质谱法和量热法。所有这些都依赖于某种方式来显示片段与酶结合，除了虚拟筛选，其中使用计算方法来尝试和识别看起来应该与酶结合的片段。一旦我们确定了与目标酶结合的片段，我们将尝试将它们培养成更大的分子。一种通用的方法是将许多片段混合，让它们以每一种可能的组合相互反应（称为动态组合化学），让酶选择出最有效结合的片段。这可能是酶作为一个模板，使两个片段结合到一起，分别结合到它。如果使用了大量的酶，可能会导致更多的关键化合物与之结合，使这种化合物被确定为主要产物。鉴定最佳结合化合物的一种更优雅的方法是在酶晶体存在下形成化合物的混合物，该方法使用较少的有价值的酶。如果一种化合物与酶结合，那么它的身份就可以通过解析酶的晶体结构来推断。我们将通过尝试制造两种酶的抑制剂来发展这些想法，这两种酶与维生素B5（泛酸）的合成有关。有证据表明，这些酶的抑制剂可能对结核病有用。靶向这些酶的另一个原因是，它们与其他酶也使用的NADPH和ATP分子结合，因此我们可能会了解一些关于如何抑制这些其他酶的有用信息。

项目成果

The Algal Chloroplast as a Testbed for Synthetic Biology Designs Aimed at Radically Rewiring Plant Metabolism.

• DOI: 10.3389/fpls.2021.708370
• 发表时间: 2021
• 期刊: Frontiers in plant science
• 影响因子: 5.6
• 作者: Jackson HO;Taunt HN;Mordaka PM;Smith AG;Purton S
• 通讯作者: Purton S

Optimization of Inhibitors of Mycobacterium tuberculosis Pantothenate Synthetase Based on Group Efficiency Analysis.

• DOI: 10.1002/cmdc.201500414
• 发表时间: 2016-01-05
• 期刊: ChemMedChem
• 影响因子: 3.4
• 作者: Hung AW;Silvestre HL;Wen S;George GP;Boland J;Blundell TL;Ciulli A;Abell C
• 通讯作者: Abell C

Fragment-based approaches to enzyme inhibition.

• DOI: 10.1016/j.copbio.2007.09.003
• 发表时间: 2007-12
• 期刊: CURRENT OPINION IN BIOTECHNOLOGY
• 影响因子: 7.7
• 作者: Ciulli, Alessio;Abell, Chris
• 通讯作者: Abell, Chris

Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate.

• DOI: 10.1002/cbic.200800437
• 发表时间: 2008-11-03
• 期刊: CHEMBIOCHEM
• 影响因子: 3.2
• 作者: Ciulli, Alessio;Scott, Duncan E.;Ando, Michiyo;Reyes, Fernando;Saldanha, S. Adrian;Tuck, Kellie L.;Chirgadze, Dimitri Y.;Blundell, Tom L.;Abell, Chris
• 通讯作者: Abell, Chris