Establishing a Gram-Negative Permeation Rule Set Leveraging a Unique Small Molecule Library

利用独特的小分子库建立革兰氏阴性渗透规则集

• 批准号: 9486473
• 负责人: Steven Armen Boyd
• 金额: $ 185.34万
• 依托单位: VENATORX PHARMACEUTICALS, INC.
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-22 至 2023-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9486473
• 关键词: Address; Anti-Bacterial Agents; Antibiotic Resistance; Antibiotics; Antimicrobial Resistance; Biochemistry; Biological; Biological Assay; Cell Membrane Permeability; Cell membrane; Cells; Characteristics; Chemicals; Clinical; Collection; Computer Simulation; Development; Diffusion; Drug Industry; Encapsulated; Engineering; Enterobacteriaceae; Escherichia coli; Exhibits; Fibrinogen; Future; Goals; Gram-Negative Bacteria; In Vitro; Industry; Knowledge; Measurable; Measures; Mediating; Membrane; Microbiology; Modeling; Molecular; Molecular Weight; Multi-Drug Resistance; Penetration; Penicillin-Binding Proteins; Permeability; Pharmaceutical Chemistry; Pharmaceutical Preparations; Pharmacologic Substance; Positioning Attribute; Probability; Process; Property; Pseudomonas aeruginosa; Publishing; Quantitative Structure-Activity Relationship; Scientist; Stratification; Structure; Talents; Therapeutic; Training; Translating; VDAC1 gene; Work; bactericide; base; beta-Lactamase; beta-Lactams; carbapenem-resistant Enterobacteriaceae; clinical practice; clinically relevant; design; direct application; drug discovery; efflux pump; exhaustion; hydrophilicity; improved; inhibitor/antagonist; innovation; multi-drug resistant pathogen; novel; pathogen; periplasm; programs; screening; small molecule; small molecule libraries; success; uptake

ABSTRACT It has been more than 30 years since the first descriptions of the relationship between molecular properties of antibiotics and their ability to accumulate within gram-negative bacteria.1,2 Considerable progress towards understanding the structure and function of porin channels mediating drug uptake and RND efflux pumps involved in drug elimination has followed.3 Yet, despite these advances, concise knowledge of the rules that define small molecule accumulation within the gram-negative cell remains elusive. As such, the antibacterial drug discovery process has reached an impasse. A solution to this discovery bottleneck is desperately needed to effectively confront the threat posed by multidrug resistant gram-negative pathogens.4 Gram-negative bacteria are encapsulated by two membranes, with the asymmetric outer membrane (OM) acting as a formidable permeability barrier to small molecules, including antibacterial drugs.5 Leaving aside mechanisms of self-promoted uptake, hydrophilic antibiotics enter gram-negative cells largely through porin channels that are believed to require increased drug polarity and low molecular weight to favor passage.6–9 Yet some antibacterial drugs do not abide by these rule.10 Therefore, there must be some level of plasticity in these rules that ultimately need to be learned and exploited. Antibacterial drug discovery would greatly benefit from establishing concise rules for periplasmic accumulation through improved outer membrane penetration. Despite exhaustive screening campaigns by drug discovery companies, progress towards this goal has been limited by a number of important factors: i) few chemical classes having measurable permeability in Gram-negatives from which to derive information, ii) minimal chemical diversity among these chemical classes and iii) a general lack of broadly applicable, biologically- relevant assays to measure small molecule accumulation in MDR gram-negative pathogens. This proposal outlines a multifaceted approach to investigate determinants of small molecule permeation in gram-negative bacteria from a unique compound collection assembled at VenatoRx Pharmaceuticals as part of drug discovery programs for β-lactamase inhibitors, Penicillin Binding Proteins. Outer membrane permeability-enabling parameters will be derived from this small molecule training set, analyzed by QSAR and Principle Component Analysis to formulate rules to guide efforts to improve periplasmic accumulation in these important pathogens. The established rule set for outer membrane penetration will be validated through direct application to an active drug discovery program for Penicillin Binding Proteins focused on Enterobacteriaceae and aiming to expand the spectrum through improved accumulation in P. aeruginosa and A. baumannii. Finally, the proposed work will focus on demystifying outer membrane permeability to relieve the bottleneck of small molecule impermeability in gram negatives and allow the rationale design of new gram-negative-biased chemical libraries to significantly improve the success rates of translating molecular screening hits into therapeutically active antibiotics.

摘要 从第一次描述分子间的关系到现在已经有30多年了， 抗生素的性质及其在革兰氏阴性菌中蓄积的能力。 了解介导药物摄取和RND外排泵的孔蛋白通道的结构和功能 然而，尽管取得了这些进展，对药物消除规则的简明知识， 确定革兰氏阴性细胞内的小分子积聚仍然是难以捉摸的。因此，抗菌剂 药物研发过程陷入僵局。迫切需要一个解决这个发现瓶颈的方案 有效应对多重耐药革兰氏阴性病原体构成的威胁。 革兰氏阴性菌由两层膜包裹，外膜不对称 (OM)作为小分子的强大渗透屏障，包括抗菌药物。 亲水性抗生素主要通过孔蛋白进入革兰氏阴性细胞， 认为需要增加药物极性和低分子量以有利于药物的通道。 一些抗菌药物不遵守这些规则。10因此，这些抗菌药物中一定存在一定程度的可塑性。 最终需要学习和利用的规则。 抗菌药物的发现将大大受益于建立简洁的规则， 通过改善外膜渗透的累积。尽管通过药物筛查活动进行了详尽的筛查， 发现公司，实现这一目标的进展受到一些重要因素的限制：i）少数 在革兰氏阴性菌中具有可测量渗透性的化学类别，从中获得信息，ii）最小 这些化学类别中的化学多样性和iii）普遍缺乏广泛适用的、生物学上的- 测量MDR革兰氏阴性病原体中小分子积累的相关测定。 该建议概述了一个多方面的方法来调查小分子渗透的决定因素 在来自VenatoRx Pharmaceuticals组装的独特化合物集合的革兰氏阴性细菌中， β-内酰胺酶抑制剂青霉素结合蛋白的药物发现项目。外膜 渗透性使能参数将从该小分子训练集导出，通过QSAR分析， 主成分分析，制定规则，以指导努力改善周质积累，在这些 重要病原体外膜渗透的既定规则集将通过直接 应用于针对肠杆菌科的青霉素结合蛋白的活性药物发现计划 并旨在通过改善铜绿假单胞菌和A.鲍曼不动杆菌。最后， 拟议的工作将集中在揭开外膜渗透性的神秘面纱，以缓解小细胞的瓶颈。 分子在革兰氏阴性中的不渗透性，并允许新的革兰氏阴性偏向化学品的合理设计 文库，以显着提高将分子筛选命中翻译成治疗的成功率。 活性抗生素