Predicting Rates and Regioselectivity in Cytochrome P450 Mediated Reactions

描述(由申请人提供)：摘要和摘要-本提案的主要目标是1)提供关于速率、区域选择性和结合方面的细胞色素P450介导的反应机制所需的基本知识，以及2)为预测ADMET的代谢成分(吸收、分布、代谢、排泄、毒性)提供计算工具。这些都是非常重要的目标，将对几乎所有药物开发项目产生积极影响，并减少开发新疗法所需的时间。这些目标将根据以下四个具体目标来描述：目标1)目前细胞色素P450所使用的活性氧物种的数量仍然存在争议，我们认为这可能解释了为什么预测新陈代谢的方法被限制在85%左右的准确性。新陈代谢预测模型在药物设计中很重要，并有可能通过减少开发新药所需的时间来拯救生命。目的2)特定目的2探索与设计成与血红素铁配合的底物的结合(类型II结合)，通过将亲和力提高250倍来提供P450酶的特异性。这一点意义重大，因为系统地给药旨在抑制单一P450酶的药物通常会导致对许多P450酶的广泛抑制，扰乱体内平衡，并导致药物-药物相互作用。目的3)P450介导率的计算预测仍然是该领域研究人员最重要的目标之一。具体目标3将确定在这种预测中重要的特征。如果这一目标能够实现，我们就可以理解预测药物从体内清除的重要特征，我们就可以更接近虚拟药物设计的目标。目标4)随着预测ADMET中计算方法和研究出版物的数量不断增加，特定目标4将提供公共的可公开访问的测试集数据库集以及开放源代码的预测代码，使不同的计算ADMET方法可以对照共同的基准进行测试。这一点尤其重要，因为大多数方法都是内部开发的，测试集没有发布。我们假设，通过将新陈代谢预测的开放源代码发布到公共网站上，我们可以将我们和其他人的研究结果转化为公共领域，从而显著提高这些工具的使用和质量。我们还假设，向所有研究人员提供一组通用的数据将鼓励验证、比较和增强ADMET模型。 公共卫生相关性：叙述--这项拨款申请的目的是了解细胞色素P450酶在药物代谢和药物设计方面的重要特征。细胞色素P450酶是最重要的药物代谢酶，负责大多数药物的代谢。虽然这个酶家族介导的大多数反应都是良性的，但也有一些会激活活性物质，从而导致癌症和毒性。此外，许多威胁生命的药物-药物相互作用发生在药物减缓细胞色素P450介导的反应。这项拨款申请将开发出比我们目前更快、更安全地设计新药的方法，方法是通过增加对速率和结合亲和力或P450介导的反应的了解。

DESCRIPTION (provided by Applicant): Summary and Abstract- The main goals of this proposal are 1) to provide the fundamental knowledge required for understanding Cytochrome P450 mediated reaction mechanism with regards to rates, regioselectivity, and binding, and 2) to provide computational tools for predicting the metabolic component of ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity). These are highly significant goals that will positively impact almost all drug development projects and decrease the time required to develop new therapeutics. These goals will be described in terms of the following four Specific Aims: Aim 1) At present the number of active-oxygen species used by Cytochrome P450 remains controversial, and we propose that this may explain why predictive methods for metabolism are limited to around 85% accuracy. Predictive models for metabolism are important in drug design, and have the potential to save lives by decreasing the time it takes to develop new drugs. Aim 2) Specific Aim 2 explores binding afforded to substrates designed to coordinate to the iron of the heme (type II binding) providing specificity for P450 enzymes by increasing affinity up to 250-fold. This is significant because systemic administration of drugs meant to inhibit a single P450 enzyme normally leads to broad inhibition of a number of P450 enzymes, upsetting homeostasis, and causing drug-drug interactions. Aim 3) Computational prediction of P450 mediated rates remains one of the most important targets of researchers working in the field. Specific Aim 3 will establish the features important in such predictions. If this goal can be met we can understand the important features involved in predicting the clearance of a drug from the body, and we move closer to the goal of virtual drug design. Aim 4) With the ever-expanding number of computational methods and research publications in predictive ADMET, Specific Aim 4 will provide common sets of publicly accessible test set databases along with open-source predictive code allowing different computational ADMET methods to be tested against common benchmarks. This is particularly important since the majority of the methods are developed in-house and the test sets are not published. We hypothesize that by publishing open source code to a public web site for metabolic predictions that we can translate the results of ours' and others' research into the public domain resulting in a significant increase in the use and quality of these tools. We also hypothesize that having a common set of data available to all researchers will encourage validation, comparison, and enhancement of ADMET models. Public Health Relevance: Narrative- The purpose of this grant application is to understand the important features of cytochrome P450 enzymes with respect to drug metabolism, and drug design. Cytochrome P450 enzymes are the most important drug metabolizing enzymes and are responsible for most drug metabolism. While the majority of the reactions mediated by this enzymes family are benign, a number cause activation to reactive species that can cause cancer and toxicity. Furthermore, many life threatening drug-drug interactions occur from drugs slowing cytochrome P450 mediated reactions. This grant application will develop methods to design new drugs faster, and safer than we can presently through an increased understanding of the rates and binding affinities or P450 mediated reactions.