Design and in situ biomanufacturing of targeted peptide inhibitors via engineered probiotic yeast.

通过工程益生菌酵母设计和原位生物制造靶向肽抑制剂。

• 批准号: 1934284
• 负责人: Nathan Crook
• 金额: $ 67.5万
• 依托单位: North Carolina State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1934284&HistoricalAwards=false
• 关键词: Design; situ; biomanufacturing; targeted; peptide

Many biological processes such as cancer cell proliferation, inflammation, and infection occur in the human gut. Biologic therapies, or treatments using substances made from living organisms, are particularly useful in treating these diseases and infections. The biological molecules used in biologic therapy tightly bind to specific molecules or organisms within the gut to modulate their behavior. Unfortunately, production and distribution of biologic therapies is incredibly complex and expensive, limiting availability to the public. A possible alternative approach is to make the biologic drugs directly in the patient's gut using unused dietary material and engineered microbes. Since the human gut is much more complex than an industrial bioreactor used to produce conventional biologics, there is still much to learn about how to accomplish this feat. This project will investigate strategies for biomanufacturing short chains of amino acids (peptides) directly in the large intestine using engineered probiotic yeast. The peptides will be optimized to bind with the toxins produced by Clostridioides difficile, the hospital-acquired gastrointestinal infection commonly referred to as C. diff. A yeast strain related to baker's yeast, Saccharomyces boulardii, will be engineered to produce the peptides under the harsh conditions of the human gut. The effectiveness of this approach will be examined in model organs, or 'miniguts.' This process of delivering drug molecules directly to the gut using engineered microbes promises to substantially reduce the cost of biologic therapeutics and, subsequently, improve human health. The investigators will also engage in research-related education and outreach, including developing a weekend symposium for high school teachers on microbiome engineering. Activities toward broadening the participation of underrepresented groups in STEM will include mentoring and active recruitment efforts. In situ biomanufacturing, wherein therapeutic molecules are synthesized directly in the human gut by engineered microbes, is an attractive alternative to the complex manufacturing and oral delivery of biologic therapies. However, the human gut is unlike any industrial bioreactor, and many outstanding questions remain before in situ biomanufacturing becomes reality. The investigators posit that manufacturing peptide-based drugs in the probiotic yeast Saccharomyces boulardii to target Clostridioides difficile infection will serve as an ideal platform and model system by which to develop design strategies enabling efficient production of biologic molecules directly in the gut. Two complementary objectives will be pursued toward testing the engineering strains and peptides. First, peptides that specifically bind to C. difficile toxin A and to its surface layer protein (SlpA) will be designed. The peptides will be designed by combining solid phase library screening and computational peptide design/optimization approaches. The efficiency of thousands of peptides will be tested using in vitro gut models. Second, the physiological state of S. boulardii in gut models will be characterized by determining which genes are expressed and which proteins are secreted while residing in the gut. This knowledge will be applied to develop engineered S. boulardii strains that can effectively secrete and display the peptides designed in the first objective. The ability of the engineered strains to counteract C. difficile pathogenesis in 3D organoids will also be determined. The project will advance understanding of in situ biomanufacturing and reveal best practices for ensuring peptide efficacy.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.

许多生物过程，如癌细胞增殖，炎症和感染发生在人类肠道中。生物疗法或使用由活生物体制成的物质的治疗在治疗这些疾病和感染中特别有用。生物疗法中使用的生物分子与肠道内的特定分子或生物体紧密结合，以调节它们的行为。不幸的是，生物疗法的生产和分销非常复杂和昂贵，限制了公众的可用性。一种可能的替代方法是使用未使用的膳食材料和工程微生物直接在患者的肠道中制造生物药物。由于人类肠道比用于生产传统生物制剂的工业生物反应器复杂得多，因此关于如何实现这一壮举还有很多东西要学。该项目将研究使用工程益生菌酵母直接在大肠中生物制造氨基酸短链（肽）的策略。这些肽将被优化以与艰难梭菌产生的毒素结合，艰难梭菌是一种医院获得性胃肠道感染，通常被称为C。diff.一种与面包酵母有关的酵母菌株，布拉酵母，将被改造成在人类肠道的恶劣条件下生产肽。这种方法的有效性将在模型器官或“小肠”中进行检验。“这种使用工程微生物将药物分子直接输送到肠道的过程有望大幅降低生物治疗的成本，并随后改善人类健康。研究人员还将参与与研究相关的教育和推广活动，包括为高中教师举办关于微生物组工程的周末研讨会。扩大代表性不足的群体参与STEM的活动将包括指导和积极的招聘工作。原位生物制造，其中治疗分子由工程微生物直接在人体肠道中合成，是复杂的制造和口服生物疗法的有吸引力的替代方案。然而，人类肠道与任何工业生物反应器不同，在原位生物制造成为现实之前，仍存在许多悬而未决的问题。研究人员认为，在益生菌酵母菌布拉酵母中生产基于肽的药物以靶向艰难梭菌感染将成为一个理想的平台和模型系统，通过该系统可以开发设计策略，从而直接在肠道中有效生产生物分子。两个互补的目标将追求对测试的工程菌株和肽。首先，特异性结合C的肽。艰难梭菌毒素A及其表面层蛋白（SlpA）将被设计。将通过结合固相文库筛选和计算肽设计/优化方法来设计肽。将使用体外肠道模型测试数千种肽的功效。第二，S.肠道模型中的布拉氏菌的特征在于确定哪些基因在肠道中表达，哪些蛋白质在肠道中分泌。这些知识将应用于开发工程S。能够有效分泌和展示在第一个目的中设计的肽的布拉氏菌菌株。工程菌对C.还将确定3D类器官中的艰难发病机制。该项目将促进对原位生物制造的理解，并揭示确保肽功效的最佳实践。该奖项反映了NSF的法定使命，并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，被认为值得支持。

项目成果

Design and in situ biosynthesis of precision therapies against gastrointestinal pathogens

• DOI: 10.1016/j.cophys.2021.06.007
• 发表时间: 2021-07-24
• 期刊: CURRENT OPINION IN PHYSIOLOGY
• 影响因子: 2.5
• 作者: Durmusoglu, Deniz;Catella, Carly M.;Crook, Nathan C.
• 通讯作者: Crook, Nathan C.

A leaky human colon model reveals uncoupled apical/basal cytotoxicity in early Clostridioides difficile toxin exposure

渗漏的人类结肠模型揭示了早期艰难梭菌毒素暴露中不偶联的顶端/基底细胞毒性

• DOI: 10.1152/ajpgi.00251.2022
• 发表时间: 2023
• 期刊: American Journal of Physiology-Gastrointestinal and Liver Physiology
• 影响因子: 4.5
• 作者: Ok, Meryem T.;Liu, Jintong;Bliton, R. Jarrett;Hinesley, Caroline M.;San Pedro, Ekaterina Ellyce;Breau, Keith A.;Gomez-Martinez, Ismael;Burclaff, Joseph;Magness, Scott T.
• 通讯作者: Magness, Scott T.

In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii

• DOI: 10.1021/acssynbio.0c00562
• 发表时间: 2021-04-12
• 期刊: ACS SYNTHETIC BIOLOGY
• 影响因子: 4.7
• 作者: Durmusoglu, Deniz;Al'Abri, Ibrahim S.;Crook, Nathan
• 通讯作者: Crook, Nathan

In Silico Identification and Experimental Validation of Peptide-Based Inhibitors Targeting Clostridium difficile Toxin A

靶向艰难梭菌毒素 A 的肽抑制剂的计算机模拟鉴定和实验验证

• DOI: 10.1021/acschembio.1c00743
• 发表时间: 2022
• 期刊: ACS Chemical Biology
• 影响因子: 4
• 作者: Xiao, Xingqing;Sarma, Sudeep;Menegatti, Stefano;Crook, Nathan;Magness, Scott T.;Hall, Carol K.
• 通讯作者: Hall, Carol K.