Core--Molecular Modeling

核心--分子建模

• 批准号: 6989519
• 负责人: MICHAEL E COLVIN
• 金额: $ 14.53万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-04-01 至 2007-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6989519
• 关键词: biomedical facility; computer simulation; immunoconjugates; immunologic substance development /preparation; molecular dynamics; neoplasm /cancer radioimmunotherapy; quantum chemistry; radiotracer; therapy design /development

The overall goal of this program project is the translational development of radioisotopic carrier molecules and strategies to deliver systemic radiotherapy for lymphomas and adenocarcinomas such as prostate cancer. The first project focuses on developing novel synthetic high affinity ligands (SHALs) that will target the Lym-1 epitope of the beta subunit of HLA-DR, known to be present on malignant lymphocytes of almost all B cell types. The second project focuses on developing novel bispecific multivalent single chain variable fragment (scFv) MAbs to be used to pretarget prostate cancer and to be followed by a small multivalent DOTA chelator of 90y. Several different types of molecular modeling has been used in support of the Projects. Homology-based protein structure prediction was used to determine: 1) the structures of HLA-DR 10, and 2) scFv MAb targeting agents, as well as 3) the scFv raised against the 90y DOTA chelator. These predicted structures were used to help identify: 1) the Lym-1 MAb epitope for subsequent computational docking studies and 2) scFv binding sites against the DOTA chelator. Quantum chemical simulations and first principles molecular dynamics simulations were used to predict the effects of chemical modifications on the structure of the 90Y-DOTA and the DOTA-DOTA linker. Finally, classical molecular dynamics were used to assist in determining the binding orientations of ligands, the design of SHALS, the optimization of the DOTA-DOTA linker and PEGylated scFv scaffold. This core component provided the computational simulation expertise and facilities to achieve these aims. All simulations were performed using computer hardware and software already available to the group. We have significant computer resources within the biology program, and extensive computer time on much larger institutional computer facilities through internal grants. The investigators selected for this Core have extensive experience in the different molecular modeling methods to be employed.

该计划项目的总体目标是放射性同位素载体分子的转化发展和为淋巴瘤和腺癌（如前列腺癌）提供全身放射治疗的策略。第一个项目的重点是开发新的合成高亲和力配体（SHAL），其将靶向HLA-DR β亚基的Lym-1表位，已知该表位存在于几乎所有B细胞类型的恶性淋巴细胞上。第二个项目的重点是开发新的双特异性多价单链可变片段（scFv）单克隆抗体，用于预靶向前列腺癌，并随后是一个小的多价DOTA螯合剂的90 y。几种不同类型的分子建模已被用于支持这些项目。基于同源性的蛋白质结构预测用于确定：1）HLA-DR 10的结构，和2）scFv MAb靶向剂，以及3）针对90 y DOTA螯合剂产生的scFv。这些预测的结构用于帮助鉴定：1）用于后续计算对接研究的Lym-1 MAb表位和2）针对DOTA螯合剂的scFv结合位点。使用量子化学模拟和第一性原理分子动力学模拟来预测化学修饰对90 Y-DOTA和DOTA-DOTA连接体的结构的影响。 最后，经典的分子动力学被用来帮助确定配体的结合方向，SHALS的设计，DOTA-DOTA接头和PEG化scFv支架的优化。这个核心组件提供了计算模拟的专业知识和设施，以实现这些目标。所有的模拟都是使用小组现有的计算机硬件和软件进行的。我们 在生物学计划中拥有重要的计算机资源，并通过内部赠款在更大的机构计算机设施上拥有大量的计算机时间。为该核心选择的研究人员在所采用的不同分子建模方法方面具有丰富的经验。