Accelerating phage evolution and tools via synthetic biology and machine learning

通过合成生物学和机器学习加速噬菌体进化和工具

• 批准号: 10443537
• 负责人: Sam R Nugen
• 金额: $ 64.32万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-16 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10443537
• 关键词: Acinetobacter baumannii; Address; Alkynes; Amino Acid Sequence; Antibiotic Resistance; Antibiotic Therapy; Antibiotics; Azides; Bacteria; Bacterial Genome; Bacterial Infections; Bacteriophage T4; Bacteriophages; Binding; Binding Proteins; Biosensing Techniques; Biosensor; CRISPR/Cas technology; Capsid; Chemistry; Clinical; Computer Models; Consumption; Custom; DNA Restriction-Modification Enzymes; Data; Data Set; Detection; Development; Diagnosis; Disease; Drug resistance; Elements; Engineering; Enterobacteriaceae; Environment; Escherichia coli; Evolution; Family; Fiber; Food; Future; Genes; Genome; Goals; Health; Human; Infection; Innate Immune Response; Innate Immune System; Intervention; Life; Literature; Machine Learning; Magnetic nanoparticles; Magnetism; Methods; Mission; Modeling; Modification; Multi-Drug Resistance; Multidrug-resistant Acinetobacter; Multiple Bacterial Drug Resistance; Natural Immunity; Outcome; Patients; Persons; Phenotype; Polyethylene Glycols; Prevention; Process; Property; Public Health; Reporting; Research; Research Personnel; Resistance; Sampling; Site; Specificity; Surface; System; Tail; Technology; Therapeutic; Therapeutic Agents; Time; Training; United States National Institutes of Health; Viral; Virus; arms race; base; design; human disease; innovation; next generation; novel; pathogen; pathogenic bacteria; rapid detection; receptor; resistance mechanism; screening; synthetic biology; therapeutically effective; tool; unnatural amino acids

Summary Phages, which are the naturally evolved predators of bacteria, may hold the key to combating bacterial pathogens, including the looming threat of multidrug resistant bacteria. Phages are viruses which while harmless to humans and have been successfully engineered as tools to separate, concentrate, and detect their bacterial hosts. Additionally, phages have been used as therapeutic agents to treat patients infected with pathogens resistant to known antibiotics. While the potential benefits of phages are numerous, certain limitations must be addressed in order to fully employ them. The central hypothesis of this proposal is that both top-down and bottom-up approaches can be utilized to design and synthesize novel phages, through a combination of synthetic biology and machine learning. This will result in phage-based tools with increased functionality and customizable host ranges. The rationale for the proposed research is that as the threat of bacterial infections including those with multi-drug resistance continues to grow, phages, which have evolved to efficiently recognize and kill bacteria, will become indispensable tools. Therefore, the ability to rapidly design and engineer new phages for biosensing and therapeutics will be a critical advantage to human health. The proposal contains three specific aims which are supported by preliminary data and cited literature. Aim 1: Site-directed conjugation for advanced phage-based biosensors and therapeutics. Under this aim, phages will be modified with alkyne-containing unnatural amino acids allowing their direct conjugation to 1) azide decorated magnetic nanoparticles, and 2) azide terminated polyethylene glycol. The modifications will allow the development of magnetic phages for bacteria separation and detection, and phages that are more effective therapeutics due to their ability to avoid a patient’s innate immune response, respectively. Aim 2: Decoding phage biorecognition elements using machine learning. In this aim, machine learning will be used to model the binding of phages and their bacterial hosts. The model will enable the prediction of host interactions as well as allow the design and synthesis of novel phage tail fibers which can target specific bacterial isolates. Aim 3: Repurposing phage biorecognition for a broader host ranges. Under the final aim, phage-binding proteins will be replaced with those known to recognize conserved regions of the bacterial LPS, resulting in a phage with a much broader host range. This approach is innovative because it uses top-down characterizations for bottom-up design and synthesis of novel phages. Traditional phage screening methods will be replaced with the rapid synthesis of phages, which are optimized for a particular bacterial isolate. Following the successful completion of the specific aims, the expected outcome is the design and synthesis of phages that can be used to target a selected group of bacteria within Enterobacteriaceae for advanced biosensing and therapeutics. A publically available computer model will allow rapid design of custom phage biorecognition elements which can be added to functionalized phages. These technologies will allow researchers to tip the scales of the co-evolutionary arms race between phage and bacteria.

总结