A Computational Approach to Developing Heterochiral Peptide Therapeutics

开发异手性肽疗法的计算方法

• 批准号: 8325624
• 负责人: Vikas Nanda
• 金额: $ 19.72万
• 依托单位: UNIV OF MED/DENT NJ-R W JOHNSON MED SCH
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-01 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8325624
• 关键词: Address; Affinity; Amino Acid Substitution; Amino Acids; Antibiotics; Area; Arsenic; Bacillus (bacterium); Bacteria; Benchmarking; Binding; Bioinformatics; Biological Factors; Blood Glucose; Cadmium; Cations; Chelation Therapy; Clinical; Cobalt; Complex; Computer-Aided Design; Computers; Databases; Development; Diabetes Mellitus; Drug Design; Drug Kinetics; Elements; Engineering; Glutamine; Hand; Hormones; Hydrogen Bonding; Insulin; Ions; Laboratories; Lead; Left; Ligands; Marketing; Medicine; Mercury; Metals; Modeling; Modification; Molecular; Molecular Conformation; Peptides; Pharmaceutical Preparations; Pharmacodynamics; Predisposition; Production; Property; Proteins; Proteolysis; Public Health; Resolution; Series; Simulate; Site; Software Design; Soil; Specificity; Structure; Testing; Therapeutic; Therapeutic Uses; Thermodynamics; Zinc Fingers; analog; antimicrobial; base; combinatorial; data mining; density; design; enantiomer; glucagon-like peptide; glucagon-like peptide 1; gramicidin A; improved; insight; macromolecule; metal poisoning; novel; peptide hormone; pre-clinical; preclinical study; programs; protein function; protein structure; public health priorities; public health relevance; scaffold; simulation; software development; success; theories; tool; toxic metal

DESCRIPTION (provided by applicant): Peptides are an emergent and important class of therapeutics with over forty compounds on the market and nearly 700 more in clinical or pre-clinical trials. During the development of peptide drugs, D-enantiomers of amino acids are frequently incorporated to improve pharmacokinetic and pharmacodynamic properties by lowering susceptibility to proteolysis. Typically, such modifications are introduced in lead compounds by trial-and-error or combinatorial approaches. Our laboratory is developing protCAD (protein Computer Aided Design) to simulate the impact of non-natural amino acids on structure and stability. Using fundamental principles of protein design, we will pursue the computational, structure-based development of peptides with variable chirality, broadly extending our capacity to create safe and potent therapeutics. The success of current computational protein design software is indebted to decades of structural and thermodynamic studies on natural proteins. This leads to an important question - Can simulation tools and molecular parameter sets these programs employ be generalized to the design of a broader class of macromolecules? Preliminary characterization of several computationally designed heterochiral proteins in our lab indicates that tools in protCAD are extendable to non-natural amino acids. In focusing on stereochemically diverse peptides, we will stringently test our fundamental understanding of principles underlying protein structure and stability. Our specific aims focus on three rationally designed, heterochiral lead scaffolds identified using a combination of protCAD and structural bioinformatics tools developed in our laboratory. Each scaffold presents a unique biophysical challenge, exploring contributions of molecular forces and the folding energy landscape in design. These scaffolds address important public health priorities including: (1) developing potent therapeutics for the treatment of diabetes, (2) providing safer molecules for chelation therapy treatment of toxic metal poisoning and (3) providing a novel, rationally designed class of antimicrobials. PUBLIC HEALTH RELEVANCE: We are developing software for the computer-based drug design of peptide therapeutics. Currently, we are focusing our program on three major areas of public health concern. The first is an anti- diabetes peptide hormone that stimulates insulin production and lowers blood sugar. We are also developing peptides that bind toxic metals to promote their safe clearance from the body. Lastly, we are adapting a natural peptide from soil bacteria to produce a new class of antibiotics. Computer engineering of peptide drugs has a lot to contribute both to medicine and to our basic understanding of how proteins function.

说明(申请人提供)：多肽是一种新兴和重要的治疗药物，市场上有40多种化合物，还有近700种化合物正在进行临床或临床前试验。在多肽药物的开发过程中，氨基酸的D-对映体经常被加入，以降低对蛋白质降解的敏感性，从而改善药代动力学和药效学性质。通常，在先导化合物中通过试错法或组合方法引入这种修饰。我们实验室正在开发ProtCAD(蛋白质计算机辅助设计)来模拟非天然氨基酸对结构和稳定性的影响。利用蛋白质设计的基本原理，我们将进行具有可变手性的多肽的计算、基于结构的开发，广泛地扩展我们创造安全和有效疗法的能力。目前计算蛋白质设计软件的成功归功于几十年来对天然蛋白质的结构和热力学研究。这引出了一个重要的问题--这些程序使用的模拟工具和分子参数集是否可以推广到更广泛类别的大分子的设计？对我们实验室中几种计算设计的杂手性蛋白质的初步表征表明，protCAD中的工具可以扩展到非天然氨基酸。在关注立体化学多样性的多肽时，我们将严格测试我们对蛋白质结构和稳定性潜在原理的基本理解。我们的具体目标是利用我们实验室开发的protCAD和结构生物信息学工具的组合来识别三种合理设计的异手性铅支架。每个支架都代表着一个独特的生物物理挑战，探索分子力的贡献和设计中的折叠能量景观。这些支架解决了重要的公共卫生优先事项，包括：(1)开发治疗糖尿病的有效疗法，(2)为螯合疗法治疗有毒金属中毒提供更安全的分子，以及(3)提供一种新型的、合理设计的抗菌剂。 与公众健康相关：我们正在开发基于计算机的多肽疗法药物设计软件。目前，我们的计划集中在公共卫生关注的三个主要领域。第一种是一种抗糖尿病的多肽荷尔蒙，它能刺激胰岛素的产生并降低血糖。我们还在开发与有毒金属结合的多肽，以促进它们在体内的安全清除。最后，我们正在改造土壤细菌中的一种天然多肽，以生产一种新的抗生素。多肽药物的计算机工程对医学和我们对蛋白质功能的基本理解都有很大的贡献。