Exploring the physicochemical properties governing compound efflux in Gram-negative bacteria

探索革兰氏阴性菌中控制化合物流出的理化特性

基本信息

批准号：
10543743
负责人：
Rebecca Ulrich
金额：
$ 4.77万
依托单位：
UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-01-16 至 2025-01-15
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10543743
关键词：
Anti-Bacterial Agents Antibiotic Resistance Antibiotics Antimicrobial Resistance Bacterial Infections Basic Science Biological Assay Cells Classification Clinical Collection Coupled Data Set Development Drug Kinetics Engineering Escherichia coli Evaluation Excision FDA approved Gram-Negative Bacteria Guidelines In Vitro Infection Informatics Libraries Measures Membrane Modeling Modification Multi-Drug Resistance Mus Nitrogen Outcome Pathogenicity Predisposition Property Quinolones Research Resistance Running Shapes Side Testing Therapeutic Toxic effect Validation Work chemical property combat design design and construction drug candidate drug resistant bacteria efficacy evaluation efficacy study efflux pump global health improved in vivo inhibitor innovation insight mouse model natural product inspired novel pathogen prevent random forest small molecule tool trait

项目摘要

Project Summary Multi-drug resistant infections are a major threat to global health and resistance has been observed for every clinically-used antibiotic, even those considered to be the last lines of treatment. Further compounding the antimicrobial resistance crisis is the lack of new antibiotics entering the pipeline, particularly for Gram- negative pathogens which have an impermeable outer membrane, limiting small molecule accumulation, and promiscuous efflux pumps, which can recognize and expel most small molecules from the cell. A basic-science understanding of favorable chemical properties required to enhance compound accumulation and decrease efflux propensity is needed to develop antibacterial candidates with whole-cell activity against Gram-negative pathogens. Initial efforts in the Hergenrother lab have identified the physicochemical traits needed for compound permeation in E. coli and successfully applied these guidelines to convert several Gram-positive only antibiotics to broad-spectrum agents. While this strategy improves Gram-negative antibacterial activity, compound efflux is still detrimental to efficacy and prevents development of these leads into potent antibiotics. It is imperative to understand the physicochemical properties governing compound recognition and efflux to provide a novel design platform to engineer efflux susceptibility out of drug candidates. The objective of this proposal is to identify the parameters that define compound efflux in Gram-negative bacteria and apply these findings to remove efflux liability out of promising antibacterial candidates. Work proposed herein will build upon preliminary studies of the efflux propensity of ~200 compounds utilizing a novel LC-MS/MS-based accumulation (Efflux Propensity EvaLuation (EXPEL)) assay which can detect small changes in efflux susceptibilities irrespective of antibacterial activity and a chemoinformatic model which can accurately classify 50% of compounds as efflux substrates and non-substrates. In Specific Aim 1, additional physicochemical properties determined important for compound efflux by the random forest model will be probed through synthesis of a targeted library of side-by-side comparisons. These compounds will be added to the dataset and iterative cycles of compound synthesis, EXPEL assay, and chemoinformatic model validation will be performed. Utilizing the EXPEL assay and the initial properties identified as correlating to efflux ratios, derivatives of an exciting FabI inhibitor will be explored to identify promising antibacterials with decreased efflux liabilities in Specific Aim 2. The therapeutic potential of these compounds will be explored through toxicity studies, determination of pharmacokinetic profile, and evaluation of efficacy in mouse infection models. Specific Aims 1 and 2 will run concurrently and completion of these studies will significantly impact antibacterial research and remedy attrition points in the antibacterial clinical pipeline.

项目概要多重耐药感染是全球健康的主要威胁，并且已观察到耐药性每一种临床使用的抗生素，甚至是那些被认为是最后一线治疗的抗生素。进一步复合抗生素耐药性危机是缺乏新的抗生素进入管道，特别是革兰氏阴性菌阴性病原体具有不可渗透的外膜，限制小分子积累，以及混杂的外排泵，可以识别细胞中的大多数小分子并将其排出。一门基础科学了解增强化合物积累和减少所需的有利化学性质开发具有针对革兰氏阴性菌的全细胞活性的抗菌候选药物需要外排倾向病原体。 Hergenrother 实验室的初步努力已经确定了所需的理化特性化合物在大肠杆菌中的渗透，并成功应用这些指南来转化几种革兰氏阳性菌仅抗生素为广谱制剂。虽然这种策略提高了革兰氏阴性菌的抗菌活性，化合物外流仍然不利于疗效并阻止这些先导化合物发展成强效抗生素。必须了解控制化合物识别和流出的物理化学特性提供一个新颖的设计平台来设计候选药物的外排敏感性。此举的目的建议是确定定义革兰氏阴性细菌中复合流出的参数并应用这些参数研究结果消除了有希望的抗菌候选药物的外排倾向。本文提出的工作将建立在对约 200 种化合物的外排倾向的初步研究的基础上利用一种新型的基于 LC-MS/MS 的累积（外排倾向评估 (EXPEL)）测定法，该测定法可以检测外排敏感性的微小变化，无论抗菌活性和化学信息学模型如何它可以准确地将 50% 的化合物分类为外排底物和非底物。在具体目标 1 中，通过随机森林模型确定对化合物流出很重要的其他物理化学特性将通过综合并排比较的目标库来探索。这些化合物将添加到数据集和化合物合成、EXPEL 测定和化学信息学模型的迭代循环中将进行验证。利用 EXPEL 测定和确定的与相关的初始特性外排比率，令人兴奋的 FabI 抑制剂的衍生物将被探索以确定有前途的抗菌药物减少特定目标 2 中的外排倾向。将探索这些化合物的治疗潜力通过毒性研究、药代动力学特征测定以及小鼠感染功效评估模型。具体目标 1 和 2 将同时进行，这些研究的完成将显着影响抗菌研究并弥补抗菌临床管道中的消耗点。