Simulation-led engineering of Diels-Alderase activity and selectivity for sustainable biosynthesis of new antibiotics

模拟主导的 Diels-Alderase 活性和选择性工程，用于新型抗生素的可持续生物合成

• 批准号: 2881671
• 金额: --
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2881671
• 关键词: Simulation; led; engineering; Diels; Alderase

Enzymes are remarkable biocatalysts that allow rapid, selective and efficient catalysis under mild conditions.Biotechnology exploits the rate-enhancing properties of these natural biocatalysts to manufacture high added-valueproducts. Of particular current interest are enzymes that catalyse the Diels-Alder reaction, a [4+2] cycloaddition reactionwidely recognised as one of the cornerstone synthetic organic reactions of the 20th century. It is commonly employed inthe synthesis of bioactive natural products, including numerous important pharmaceuticals. Without enzyme biocatalysts,harsh reaction conditions (high temperature, high pressure) often must be employed, and precise control over the productoutcome is limited. Enzymes that catalyse this reaction, Diels-Alderases, are therefore highly attractive. In this project, the focus will be on Diels-Alderases involved in the biosynthesis of tetronate antibiotics such asabyssomicins, natural products with highly promising antibiotic activity. We have already established the structure andmechanism of two of these in detail, for which computational simulation, including docking, molecular dynamicsand QM/MM reaction simulations, has proven highly valuable. The same is true for crucial tailoring enzymes that arerequired before and after the Diels-Alderase step to arrive at the active polyketide-based antibiotic. The project aims touse these techniques in new computational prediction protocols that can suggest enzyme variants with desired changesin activity and specifity, for example to obtain tetronate antiobiotics with improved characteristics for pharmaceuticaluse. To test and improve these predictions, experimental characterisation of promising enzyme variants (productoutcome, kinetics and structural biology) will be performed. By working with our industrial partner AstraZeneca, theimpact of engineered enzymes can be realised by testing their use for generating valuable building blocks and scaffolds forpharmaceutical drug discovery. This interdisciplinary project combines the expertise in computational simulation ofenzymes in Bristol and the expertise from an internationally leading academic team with multidisciplinary expertise ofpolyketide natural product biosynthesis and relevant experimental techniques (enzymology, molecular biology,chemistry and structural biology).Combining simulation and experiment in this way is still developing, but will become increasingly important; in Bristol, weare at the forefront of this development. The multidisciplinary environment ensures the student will acquire a range ofskills that will arm them for a future career in academic or industrial bioscience (including pharmaceutical science). Thestudent will be embedded in the vibrant research environment in Bristol, including the Centre for ComputationalChemistry and the Bristol BioDesign institute, ensuring a wide range of interactions, seminar programmes and courses.

酶是卓越的生物催化剂，可在温和条件下实现快速、选择性和高效的催化作用。生物技术利用这些天然生物催化剂的提速特性来制造高附加值产品。目前特别感兴趣的是催化狄尔斯-阿尔德反应的酶，这是一种[4+2]环加成反应，被广泛认为是 20 世纪合成有机反应的基石之一。它通常用于合成生物活性天然产物，包括许多重要的药物。如果没有酶生物催化剂，往往必须采用苛刻的反应条件（高温、高压），并且对产品结果的精确控制受到限制。因此，催化该反应的酶（狄尔斯-阿尔德酶）非常有吸引力。在该项目中，重点将放在参与特酮酸抗生素生物合成的 Diels-Alderases，例如阿萨比索霉素（asabyssomicins），这是一种具有高度前景的抗生素活性的天然产物。我们已经详细建立了其中两个的结构和机制，其中计算模拟，包括对接、分子动力学和 QM/MM 反应模拟，已被证明非常有价值。对于在 Diels-Alderase 步骤之前和之后获得活性聚酮化合物抗生素所需的关键定制酶也是如此。该项目旨在在新的计算预测方案中使用这些技术，该方案可以建议具有所需活性和特异性变化的酶变体，例如获得具有改进的药用特性的特酮酸抗生素。为了测试和改进这些预测，将对有前景的酶变体（产品结果、动力学和结构生物学）进行实验表征。通过与我们的工业合作伙伴阿斯利康合作，可以通过测试工程酶为药物发现生成有价值的构建块和支架的用途来实现工程酶的影响。这个跨学科项目结合了布里斯托尔在酶计算模拟方面的专业知识以及国际领先的学术团队的专业知识，他们具有聚酮化合物天然产物生物合成和相关实验技术（酶学、分子生物学、化学和结构生物学）的多学科专业知识。方式仍在发展，但将变得越来越重要；在布里斯托尔，我们处于这一发展的最前沿。多学科环境确保学生获得一系列技能，为他们未来从事学术或工业生物科学（包括制药科学）职业做好准备。学生将融入布里斯托尔充满活力的研究环境，包括计算化学中心和布里斯托尔生物设计研究所，确保广泛的互动、研讨会项目和课程。