A Mechanism Based Approach to Metallo beta-lactamase Inhibition

项目来源

美国卫生和人类服务部基金(HHS)

项目主持人

XU, ZUOYU

项目受资助机构

CASE WESTERN RESERVE UNIVERSITY

立项年度

2019

立项时间

未公开

项目编号

5R01AI100560-07

项目级别

国家级

研究期限

未知 / 未知

受资助金额

474827.00美元

学科

Antimicrobial Resistance; Biodefense; Emerging Infectious Diseases; Infectious Diseases;

学科代码

未公开

基金类别

Non-SBIR/STTR RPGs

关键词

未公开

参与者

BONOMO, ROBERT A. ; SPENCER, JAMES ; VILA, ALEJANDRO J

参与机构

NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES

项目标书摘要:Gram-negative pathogens producing metallo-?-lactamases, MBLs, seriously threaten the public health. MBLs are the most worrisome carbapenemases, inactivating the ?last resort? carbapenems and most ?-lactams, and resist all commercially available ?-lactamase inhibitors (BLIs). The main challenges in MBL inhibitor design are understanding the reaction mechanism as it relates to the structural diversity of the 3 distinct subclasses (B1, B2, and B3). In the previous 5-year funding cycle, we achieved important milestones: i) identified the active form of clinically relevant MBLs in the bacterial periplasm; ii) characterized NDM-1 as a membrane-bound protein, establishing how this localization endows NDM-1 with unique stability; iii) demonstrated that MBLs of all 3 subclasses utilize a common mechanism for carbapenem hydrolysis suggesting novel approaches for inhibitor development; iv) designed a series of novel compounds, bisthiazolidines (BTZs), as substrate mimics, comprising a non- ?-lactam ?penicillin core? decorated with metal binding groups; and v) showed that BTZs are non-toxic, effective cross-class MBL inhibitors and identified the structural bases of their inhibitory action. Responding to the clear urgency to find novel therapies, our team will build on these accomplishments to identify, synthesize, evaluate and develop new cross-class MBL inhibitors. Our unique approach is based upon a mechanistic understanding of MBL catalysis which will be utilized to inspire potent inhibitors. To this end, we will synthesize new compounds as mimics of mechanistic intermediates or product mimics [Thiazolidines (TZs), ?4- Thiazolidines (?4-TZs), and ?4-Oxazolidines (?4-OXZs)] or carbapenem mimics [?4-Bisthiazolidines (?4-BTZs) and Bicyclooctanes (BCOs)]. Our second specific aim will evaluate inhibitors for in vitro activity against MBLs of all subclasses. We will next assay the impact of inhibitors in potentiating ?-lactam efficacy against MBL- producing model strains, assess differences between in vitro assays and effect on bacteria, and validate the selected inhibitors against a panel of clinical strains with different MBL alleles. Our third aim will combine NMR and X-ray crystallography to study the structure of MBL-inhibitor adducts aimed to provide details for inhibitor improvement. We will also pursue mechanistic studies using micro-focusing spectroscopy and crystallography coupled to XFEL (X-ray free electron lasers) to trap transient ?-lactam-bound species in the enzymes NDM-1, L1, and VIM. This ?high-risk, high impact? innovative approach using new technologies will provide information for inhibitor improvement. Lastly, we will assay off-target activity and in vitro toxicity of the synthesized compounds, perform time-kill assays for meropenem-BLI combinations in clinical strains; and use mouse blood stream and lung infection models to assess the in vivo potency of meropenem/MBL-inhibitor combinations. This knowledge will serve to inform the design of therapeutic leads to combat MBL producing bacteria.

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  • 1.Exploring Additional Dimensions of Complexity in Inhibitor Design for Serine beta-Lactamases: Mechanistic and Intra- and Inter-molecular Chemistry Approaches

    • 关键词:
    • beta-lactamase; structural biology; enzyme inhibitors; transition state;antibacterial agents;6-(1-HYDROXYALKYL)PENAM SULFONE DERIVATIVES; TRANS-ENAMINE INTERMEDIATE;GRAM-NEGATIVE BACTERIA; CLASS-A; CRYSTAL-STRUCTURES; BORONIC ACID; PENAMSULFONES; CRYSTALLOGRAPHIC STRUCTURES; DEACYLATION MECHANISM;6-METHYLIDENE PENEMS

    As a bacterial resistance strategy, serine beta-lactamases have evolved from cell wall synthesizing enzymes known as penicillin-binding proteins (PBP), by not only covalently binding beta-lactam antibiotics but, also acquiring mechanisms of deacylating these antibiotics. This critical deacylation step leads to release of hydrolyzed and inactivated beta-lactams, thereby providing resistance for the bacteria against these antibiotics targeting the cell wall. To combat beta-lactamase-mediated antibiotic resistance, numerous beta-lactamase inhibitors were developed that utilize various strategies to inactivate the beta-lactamase. Most of these compounds are "mechanism-based" inhibitors that in some manner mimic the beta-lactam substrate, having a carbonyl moiety and a negatively charged carboxyl or sulfate group. These compounds form a covalent adduct with the catalytic serine via an initial acylation step. To increase the life-time of the inhibitory covalent adduct intermediates, a remarkable array of different strategies was employed to improve inhibition potency. Such approaches include post-acylation intra- and intermolecular chemical rearrangements as well as affecting the deacylation water. These approaches transform the inhibitor design process from a 3-dimensional problem (i.e., XYZ coordinates) to one with additional dimensions of complexity as the reaction coordinate and time spent at each chemical state need to be taken into consideration. This review highlights the mechanistic intricacies of the design efforts of the beta-lactamase inhibitors which so far have resulted in the development of "two generations" and 5 clinically available inhibitors.

    ...
  • 3.Precision Medicine and Mysteries in Clinical Microbiology: Rationalizing Epidemiology, Genotype, and Phenotype To Guide Therapeutics

    • 关键词:
    • PLASMIDS

    Whole-genome sequencing (WGS) using MinION was used to characterize high-risk clones of Escherichia coli and Klebsiella pneumoniae harboring bla(NDM-5), bla(OXA-181), and bla(CTX-M-15), as well as Pseudomonas aeruginosa harboring bla(NDM), in a patient who received health care in India. Synergy testing demonstrated the activity of aztreonam and ceftazime-avibactam in combination. This case illustrates a "precision medicine" approach where deeper understanding of the genotype through WGS and of the phenotype through synergy testing formed the basis for rational combination therapy.

    ...
  • 4.A Primer on AmpC beta-Lactamases: Necessary Knowledge for an Increasingly Multidrug-resistant World

    • 关键词:
    • Enterobacter cloacae; antimicrobial resistance; Citrobacter freundii;Serratia marcescens;EXTENDED-SPECTRUM CEPHALOSPORINS; GRAM-NEGATIVE BACILLI;ENTEROBACTER-CLOACAE; KLEBSIELLA-PNEUMONIAE; CITROBACTER-FREUNDII;ESCHERICHIA-COLI; ANTIMICROBIAL SUSCEPTIBILITY; ANTIBACTERIAL ACTIVITY;ANTIBIOTIC-RESISTANCE; MORGANELLA-MORGANII

    Understanding the nuances of AmpC beta-lactamase-mediated resistance can be challenging, even for the infectious diseases specialist. AmpC resistance can be classified into 3 categories: (1) inducible chromosomal resistance that emerges in the setting of a beta-lactam compound, (2) stable derepression due to mutations in ampC regulatory genes, or (3) the presence of plasmid-mediated ampC genes. This review will mainly focus on inducible AmpC resistance in Enterobacteriaceae. Although several observational studies have explored optimal treatment for AmpC producers, few provide reliable insights into effective management approaches. Heterogeneity within the data and inherent selection bias make inferences on effective beta-lactam choices problematic. Most experts agree it is prudent to avoid expanded-spectrum (ie, third-generation) cephalosporins for the treatment of organisms posing the greatest risk of ampC induction, which has best been described in the context of Enterobacter cloacae infections. The role of other broad-spectrum beta-lactams and the likelihood of ampC induction by other Enterobacteriaceae are less clear. We will review the mechanisms of resistance and triggers resulting in AmpC expression, the species-specific epidemiology of AmpC production, approaches to the detection of AmpC production, and treatment options for AmpC-producing infections.

    ...
  • 5.The Continuing Challenge of Metallo-beta-Lactamase Inhibition: Mechanism Matters

    • 关键词:
    • VARIANTS REVEALS DIFFERENCES; BROAD-SPECTRUM INHIBITOR;CONFORMATIONAL-CHANGES; KLEBSIELLA-PNEUMONIAE; STRUCTURAL BASIS;ACTIVE-SITE; BINDING; ZINC; NMR; EPR

    Metallo-beta-lactamases (MBLs) are a significant clinical problem because they hydrolyze and inactivate nearly all beta-lactann-containing antibiotics. These 'lifesaving drugs' constitute >50% of the available contemporary antibiotic arsenal. Despite the global spread of MBLs, MBL inhibitors have not yet appeared in clinical trials. Most MBL inhibitors target active site zinc ions and vary in mechanism from ternary complex formation to metal ion stripping. Importantly, differences in mechanism can impact pharmacology in terms of reversibility, target selectivity, and structure activity relationship interpretation. This review surveys the mechanisms of MBL inhibitors and describes methods that determine the mechanism of inhibition to guide development of future therapeutics.

    ...
  • 6.Therapies for multidrug resistant and extensively drug-resistant non-fermenting gram-negative bacteria causing nosocomial infections: a perilous journey toward "molecularly targeted' therapy

    • 关键词:
    • Gram-negative bacteria; glucose-non-fermenting; antimicrobialresistance; nosocomial infections; mechanisms of resistance; combinationtherapy; precision medicine;BURKHOLDERIA-CEPACIA-COMPLEX; BLOOD-STREAM INFECTION; IN-VITRO ACTIVITY;PSEUDOMONAS-AERUGINOSA INFECTION; ACINETOBACTER-BAUMANNII BACTEREMIA;VENTILATOR-ASSOCIATED PNEUMONIA; CRITICALLY-ILL PATIENTS; HIGH-DOSETIGECYCLINE; STENOTROPHOMONAS-MALTOPHILIA; COMBINATION THERAPY

    Introduction: Non-fermenting Gram-negative bacilli are at the center of the antimicrobial resistance epidemic. Acinetobacter baumannii and Pseudomonas aeruginosa are both designated with a threat level to human health of serious' by the Centers for Disease Control and Prevention. Two other major non-fermenting Gram-negative bacilli, Stenotrophomonas maltophilia and Burkholderia cepacia complex, while not as prevalent, have devastating effects on vulnerable populations, such as those with cystic fibrosis, as well as immunosuppressed or hospitalized patients.Areas covered: In this review, we summarize the clinical impact, presentations, and mechanisms of resistance of these four major groups of non-fermenting Gram-negative bacilli. We also describe available and promising novel therapeutic options and strategies, particularly combination antibiotic strategies, with a focus on multidrug resistant variants.Expert commentary: We finally advocate for a therapeutic approach that incorporates in vitro antibiotic susceptibility testing with molecular and genotypic characterization of mechanisms of resistance, as well as pharmacokinetics and pharmacodynamics (PK/PD) parameters. The goal is to begin to formulate a precision medicine approach to antimicrobial therapy: a clinical-decision making model that integrates bacterial phenotype, genotype and patient's PK/PD to arrive at rationally-optimized combination antibiotic chemotherapy regimens tailored to individual clinical scenarios.

    ...
  • 7.The Continuing Challenge of Metallo-beta-Lactamase Inhibition: Mechanism Matters

    • 关键词:
    • VARIANTS REVEALS DIFFERENCES; BROAD-SPECTRUM INHIBITOR;CONFORMATIONAL-CHANGES; KLEBSIELLA-PNEUMONIAE; STRUCTURAL BASIS;ACTIVE-SITE; BINDING; ZINC; NMR; EPR

    Metallo-beta-lactamases (MBLs) are a significant clinical problem because they hydrolyze and inactivate nearly all beta-lactann-containing antibiotics. These 'lifesaving drugs' constitute >50% of the available contemporary antibiotic arsenal. Despite the global spread of MBLs, MBL inhibitors have not yet appeared in clinical trials. Most MBL inhibitors target active site zinc ions and vary in mechanism from ternary complex formation to metal ion stripping. Importantly, differences in mechanism can impact pharmacology in terms of reversibility, target selectivity, and structure activity relationship interpretation. This review surveys the mechanisms of MBL inhibitors and describes methods that determine the mechanism of inhibition to guide development of future therapeutics.

    ...
  • 8.Therapies for multidrug resistant and extensively drug-resistant non-fermenting gram-negative bacteria causing nosocomial infections: a perilous journey toward "molecularly targeted' therapy

    • 关键词:
    • Gram-negative bacteria; glucose-non-fermenting; antimicrobialresistance; nosocomial infections; mechanisms of resistance; combinationtherapy; precision medicine;BURKHOLDERIA-CEPACIA-COMPLEX; BLOOD-STREAM INFECTION; IN-VITRO ACTIVITY;PSEUDOMONAS-AERUGINOSA INFECTION; ACINETOBACTER-BAUMANNII BACTEREMIA;VENTILATOR-ASSOCIATED PNEUMONIA; CRITICALLY-ILL PATIENTS; HIGH-DOSETIGECYCLINE; STENOTROPHOMONAS-MALTOPHILIA; COMBINATION THERAPY

    Introduction: Non-fermenting Gram-negative bacilli are at the center of the antimicrobial resistance epidemic. Acinetobacter baumannii and Pseudomonas aeruginosa are both designated with a threat level to human health of serious' by the Centers for Disease Control and Prevention. Two other major non-fermenting Gram-negative bacilli, Stenotrophomonas maltophilia and Burkholderia cepacia complex, while not as prevalent, have devastating effects on vulnerable populations, such as those with cystic fibrosis, as well as immunosuppressed or hospitalized patients.Areas covered: In this review, we summarize the clinical impact, presentations, and mechanisms of resistance of these four major groups of non-fermenting Gram-negative bacilli. We also describe available and promising novel therapeutic options and strategies, particularly combination antibiotic strategies, with a focus on multidrug resistant variants.Expert commentary: We finally advocate for a therapeutic approach that incorporates in vitro antibiotic susceptibility testing with molecular and genotypic characterization of mechanisms of resistance, as well as pharmacokinetics and pharmacodynamics (PK/PD) parameters. The goal is to begin to formulate a precision medicine approach to antimicrobial therapy: a clinical-decision making model that integrates bacterial phenotype, genotype and patient's PK/PD to arrive at rationally-optimized combination antibiotic chemotherapy regimens tailored to individual clinical scenarios.

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