Characterization of MsbA inhibitors as potential antibiotic leads to treat carbapenem-resistant Enterobacteriaceae (CRE)

MsbA 抑制剂作为潜在抗生素的特性可用于治疗耐碳青霉烯类肠杆菌 (CRE)

• 批准号: 9978345
• 负责人: Terry Roemer
• 金额: $ 24.5万
• 依托单位: PROKARYOTICS, INC.
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-19 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9978345
• 关键词: ATP phosphohydrolase; ATP-Binding Cassette Transporters; Address; American; Aminoglycosides; Anti-Bacterial Agents; Antibiotics; Bacterial Drug Resistance; Bacterial Infections; Binding Sites; Biochemical; Biogenesis; Biological Assay; CDC2 gene; Carbapenems; Cell Survival; Cells; Cellular Structures; Centers for Disease Control and Prevention (U.S.); Cephalosporins; Chemicals; Clinical; Coculture Techniques; Colistin; Collaborations; Communicable Diseases; Communities; Complex; Cryoelectron Microscopy; Crystallization; Data; Deacetylase; Development; Dose; Drug Design; Enterobacter; Enterobacteriaceae; Enterobacteriaceae Infections; Enzymes; Escherichia coli; Escherichia coli drug resistance; European; Fosfomycin; Foundations; Fright; Future; Genomic Centers for Infectious Diseases; Goals; Gram-Negative Bacteria; Health Care Costs; HepG2; Hospitals; In Vitro; Klebsiella pneumoniae; Lactamase; Lactams; Lead; Left; Length of Stay; Letters; Life; Ligand Binding; Lipopolysaccharide Biosynthesis Pathway; Lipopolysaccharides; Mediating; Membrane; Meropenem; Microbiology; Molecular Conformation; Multi-Drug Resistance; Mutation; New Agents; Oral; Organism; Pathway interactions; Pattern; Permeability; Pharmaceutical Chemistry; Pharmaceutical Preparations; Polymyxins; Proteins; Reporting; Resistance; Resolution; Risk; Roentgen Rays; Series; Siderophores; Solid; Structure; Structure-Activity Relationship; Superbug; Tetracyclines; Therapeutic; Time; Zinc; antimicrobial; bactericide; base; beta-Lactam Resistance; carbapenem resistance; carbapenem-resistant Enterobacteriaceae; clinically relevant; commensal bacteria; doripenem; genome sequencing; gut microbiota; improved; in vitro activity; inhibitor/antagonist; innovation; lead optimization; membrane biogenesis; molecular site; mortality; mutant; novel; novel therapeutics; overexpression; pathogen; periplasm; resistance frequency; small molecule inhibitor; structural genomics; tigecycline; whole genome

In 2013, the CDC designated carbapenem-resistant Enterobacteriaceae (CRE) an Urgent Threat, and in 2017, the WHO designated it a Priority 1 “critical superbug”. As few therapies remain to treat CRE, the risk of “pan- resistant” CRE untreatable by any currently available antibiotic also exists. Entirely new agents with novel mechanisms of action (MOA) not cross-resistant to SOC agents languish. Development of such a ‘first-in-class’ agent also offers the potential for much-needed orally-administered CRE therapeutic, thus providing a new step-down therapy to reduce hospital stay and growing healthcare costs. Our proposal aims to develop an entirely novel therapeutic to treat life-threatening bacterial infections due to multidrug resistant (MDR) Enterobacteriaceae, including CRE. Using an innovative overexpression-based co-culture screen in Escherichia coli (Ec), we identified four structurally distinct series of small molecule inhibitors targeting MsbA, an essential and broadly conserved Gram-negative (GN) ABC transporter responsible for lipopolysaccharide (LPS) biogenesis and construction of the Gram-negative outer membrane (OM). Building upon a solid foundation of preliminary data, our Aims are: Aim (A) 1. Expanded MOA studies. Aim 1 studies will expand upon our preliminary MOA and microbiological characterization of the MsbA inhibitor (MsbAi) hits to include other GN bacteria, particularly Klebsiella pneumoniae (Kp). Specifically, we will demonstrate Kp MsbA target inhibition in (1) an in vitro biochemical assay and (2) a whole-cell context by determining MICs of our MsbAis against a Kp tolC strain and subsequently selecting for MsbAisR mutants in this Kp background. Aim 2. Demonstrate chemical tractability of MsbAis. The goal of Aim 2 is to perform Hit to Lead (H2L) medicinal chemistry structure activity relationship (SAR) studies for each MsbAi and demonstrate >1 series is chemically tractable and that quantifiable pre-lead optimization criteria can be established, including i) Ec and Kp MsbA in vitro potency (IC50 < 0.25 µg/ml), ii) Ec and Kp WT activity (<16 µg/ml), and iii) > 90% HepG2 cell viability at 50X MIC against EcΔtolC. MsbAis achieving these milestones serve as a justifiable starting point for a future Lead Optimization leveraging the resulting SAR gained in Aim 2 and SBDD information from Aim 3. Aim 3. Obtain Ec and Kp MsbAi-MsbA co-crystal structures in collaboration with SSGCID. The goal of Aim 3 activities is to initiate a collaboration between Prokaryotics, Genentech, and the Seattle Structural Genomics Center for Infectious Disease (SSGCID) led by Dr. Peter Myler to optimize conditions suitable for obtaining high resolution x-ray crystal structures of Kp MsbA in the apo form as well as Ec and/or Kp MsbA proteins in complex with MsbAis.

2013年，CDC将碳青霉烯抗性肠杆菌科（CRE）列为紧急威胁，2017年，