Metagenomic discovery and optimization of novel endolysins targeting Cutibacterium acnes to treat acne vulgaris

针对痤疮皮肤杆菌治疗寻常痤疮的新型内溶素的宏基因组发现和优化

• 批准号: 10821291
• 负责人: Oliver Wei Liu
• 金额: $ 27.53万
• 依托单位: TOPAZ BIOSCIENCES, INC.
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-15 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10821291
• 关键词: Acne; Acne Vulgaris; Affect; Antibiotic Resistance; Antibiotic Therapy; Antibiotics; Anxiety; Bacteria; Bacteriophages; Benchmarking; Binding; Bioinformatics; Biological Assay; Biological Sciences; Cell Wall; Chimeric Proteins; Codon Nucleotides; Cultural Diversity; Data Set; Databases; Development; Engineering; Environment; Enzymes; Epitopes; Feeling suicidal; Gardnerella vaginalis; Genome; Hydrolase; Immunologic Stimulation; Length; Libraries; Lytic; Measurement; Mental Depression; Metagenomics; Oral; Pathogenesis; Pathogenicity; Persons; Phase; Play; Property; Prophages; Proteins; Recombinant Proteins; Reproducibility; Role; Soil; Solubility; Source; Specificity; Staphylococcus aureus; Topaz; antimicrobial; antimicrobial drug; design; domain walls; endolysin; gut microbiome; improved; insight; novel; preservation; protein B; protein purification; psychosocial; self esteem; skin microbiome; synthetic biology; thermostability

PROJECT SUMMARY Acne vulgaris (acne) affects up to 50 million people in the U.S. annually and can have significant negative consequences on psychosocial functioning including higher rates of anxiety, low self-esteem, depression, and suicidal ideation. Cutibacterium acnes plays a central role in acne pathogenesis and it is now understood that a decrease in C. acnes phylotype diversity and an increase in the homogeneity of the pathogenic phylotype IA1 triggers innate immune stimulation and acne progression. Topical and oral antibiotics to target C. acnes remain part of first-line treatments for acne, but continued use of antibiotics poses significant challenges including exacerbation of antibiotic resistance as well as collateral damage to the healthy commensals in the gut and skin microbiomes. Given these drawbacks, novel antimicrobial agents that can provide alternatives to antibiotics and selectively target C. acnes without damaging beneficial bacteria are needed. Endolysins are phage-encoded enzymes that can degrade bacterial cell walls. Exogenously added endolysins can quickly lyse their target bacteria and because they bind very specific epitopes in target cell walls, they can have lytic specificity down to a single species or even sub-species. Given these properties, endolysins hold enormous potential as high-specificity skin microbiome modulators. However, the diversity of endolysins known to target C. acnes is low and these enzymes suffer from low activity and low solubility. Recent metagenomic analyses demonstrate that Cutibacterium sp. are found ubiquitously in the soil and that these environments can provide a rich, untapped source of Cutibacterium diversity. At Topaz Biosciences, we have developed a proprietary metagenomic platform for the discovery and optimization of endolysins. We have previously leveraged this platform to develop endolysins against Staphylococcus aureus that are more active, more thermostable, and have a broader pH range than benchmark enzymes. In this Phase I proposal, we will leverage this platform to expand the diversity of endolysins known to have activity against C. acnes and then exploit this diversity to develop chimeric enzymes with improved properties. To accomplish this, we will take advantage of the modularity of endolysins to build a library of endolysin “parts” – enzymatic domains (EADs) and cell wall binding domains (CBDs) that we will systemically characterize for anti-Cutibacterium activity, thermostability, and pH tolerance. An initial set of “parts” will come from sequenced Cutibacterium genomes and phages. Then, to significantly expand the diversity of EADs and CBDs, we will computationally select ~200 diverse endolysins/domains predicted to have anti-Cutibacterium activity from proprietary and public metagenomic databases for additional characterization. Finally, we will leverage sequence-function insights gained from our “parts” development to design chimeric endolysins composed of EADs and CBDs with the most promising properties to generate enzyme candidates that demonstrate improved activity, solubility, thermostability, and pH range.

项目摘要 痤疮的痤疮（痤疮）每年在美国影响多达5000万人，并且可能有明显的负面影响 对社会心理功能的后果，包括更高的动画率，低自尊，抑郁和 自杀的想法。 cutibacterium痤疮在痤疮发病机理中起着核心作用，现在已经了解 痤疮梭菌的系统型多样性的降低和致病系统型IA1的均匀性的增加 触发先天免疫刺激和痤疮进展。靶向痤疮的局部和口服抗生素仍然存在 痤疮一线治疗的一部分，但继续使用抗生素有重大挑战 加剧抗生素耐药性以及对肠道健康份额的附带损害 皮肤微生物组。鉴于这些缺点，可以为您提供替代品的新型抗菌剂 需要抗生素和选择性地靶向痤疮杆菌，而无需损害有益细菌。 内olysin是噬菌体编码的酶，可降解细菌细胞壁。外源添加的内olysins 可以快速裂解其靶细菌，并且由于它们结合了目标细胞壁中非常特异的表位，因此可以 具有裂解特异性至单个物种甚至亚种。鉴于这些特性，内叶蛋白保持 作为高特异性皮肤微生物组调节剂的巨大潜力。但是，内叶素的多样性 靶向痤疮杆菌已知的较低，这些酶的活性低和溶解度低。最近的 宏基因组分析表明Cutibacterium sp。在土壤中普遍存在，这些 环境可以提供丰富的，未开发的cutibacterium多样性来源。 在Topaz Biosciences，我们为发现和 内叶蛋白的优化。我们以前已经利用了这个平台来开发内叶素反对 金黄色葡萄球菌更活跃，更热，并且pH范围更宽 基准酶。在此阶段我的建议中，我们将利用该平台扩大 内olysin已知具有针对痤疮梭菌的活性，然后利用这种多样性来发展嵌合 具有改善特性的酶。为此，我们将利用 内叶蛋白要建立一个内olysin“零件”的库 - 酶域（EADS）和细胞壁绑定域 （CBD）我们将系统地表征抗核酸杆菌活性，热稳定性和pH耐受性。 一组“零件”将来自测序的cutibacterium基因组和噬菌体。然后，要大量 扩大EAD和CBD的多样性，我们将在计算上选择〜200个潜水员的内叶素/域 预计具有专有和公共元基因组数据库的抗细菌活性 表征。最后，我们将利用从“零件”开发获得的序列功能见解到 设计嵌合内叶蛋白，由EAD和CBD组成，具有最有前途的特性 酶的酶候选物显示出改善的活性，可溶性，热稳定性和pH范围。