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Al-Madboly LA, El-Salam MAA, Bastos JK, Aboukhatwa S, El-Morsi RM. Characterization of GQA as a novel β-lactamase inhibitor of CTX-M-15 and KPC-2 enzymes. Microb Cell Fact 2024; 23:221. [PMID: 39118086 PMCID: PMC11308155 DOI: 10.1186/s12934-024-02421-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/11/2024] [Indexed: 08/10/2024] Open
Abstract
β-lactam resistance is a significant global public health issue. Outbreaks of bacteria resistant to extended-spectrum β-lactams and carbapenems are serious health concerns that not only complicate medical care but also impact patient outcomes. The primary objective of this work was to express and purify two soluble recombinant representative serine β‑lactamases using Escherichia coli strain as an expression host and pET101/D as a cloning vector. Furthermore, a second objective was to evaluate the potential, innovative, and safe use of galloylquinic acid (GQA) from Copaifera lucens as a potential β-lactamase inhibitor.In the present study, blaCTX-M-15 and blaKPC-2 represented genes encoding for serine β-lactamases that were cloned from parent isolates of E. coli and K. pneumoniae, respectively, and expression as well as purification were performed. Moreover, susceptibility results demonstrated that recombinant cells became resistant to all test carbapenems (MICs; 64-128 µg/mL) and cephalosporins (MICs; 128-512 µg/mL). The MICs of the tested β-lactam antibiotics were determined in combination with 4 µg/mL of GQA, clavulanic acid, or tazobactam against E. coli strains expressing CTX-M-15 or KPC-2-β-lactamases. Interestingly, the combination with GQA resulted in an important reduction in the MIC values by 64-512-fold to the susceptible range with comparable results for other reference inhibitors. Additionally, the half-maximal inhibitory concentration of GQA was determined using nitrocefin as a β-lactamase substrate. Data showed that the test agent was similar to tazobactam as an efficient inhibitors of the test enzymes, recording smaller IC50 values (CTX-M-15; 17.51 for tazobactam, 28.16 µg/mL for GQA however, KPC-2; 20.91 for tazobactam, 24.76 µg/mL for GQA) compared to clavulanic acid. Our work introduces GQA as a novel non-β-lactam inhibitor, which interacts with the crucial residues involved in β-lactam recognition and hydrolysis by non-covalent interactions, complementing the enzyme's active site. GQA markedly enhanced the potency of β-lactams against carbapenemase and extended-spectrum β-lactamase-producing strains, reducing the MICs of β-lactams to the susceptible range. The β-lactamase inhibitory activity of GQA makes it a promising lead molecule for the development of more potent β-lactamase inhibitors.
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Affiliation(s)
- Lamiaa A Al-Madboly
- Department of Microbiology and Immunology, Faculty of Pharmacy, Tanta University, Tanta, Egypt.
| | - Mohamed A Abd El-Salam
- Department of Pharmacognosy, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa, 11152, Egypt.
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, D02 VN51, Ireland.
| | - Jairo K Bastos
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, SP, 14040-903, Brazil
| | - Shaimaa Aboukhatwa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Rasha M El-Morsi
- Department of Microbiology and Immunology, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa, 11152, Egypt
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2
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Koenig C, Kuti JL. Evolving resistance landscape in gram-negative pathogens: An update on β-lactam and β-lactam-inhibitor treatment combinations for carbapenem-resistant organisms. Pharmacotherapy 2024; 44:658-674. [PMID: 38949413 DOI: 10.1002/phar.2950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/24/2024] [Accepted: 05/25/2024] [Indexed: 07/02/2024]
Abstract
Antibiotic resistance has become a global threat as it is continuously growing due to the evolution of β-lactamases diminishing the activity of classic β-lactam (BL) antibiotics. Recent antibiotic discovery and development efforts have led to the availability of β-lactamase inhibitors (BLIs) with activity against extended-spectrum β-lactamases as well as Klebsiella pneumoniae carbapenemase (KPC)-producing carbapenem-resistant organisms (CRO). Nevertheless, there is still a lack of drugs that target metallo-β-lactamases (MBL), which hydrolyze carbapenems efficiently, and oxacillinases (OXA) often present in carbapenem-resistant Acinetobacter baumannii. This review aims to provide a snapshot of microbiology, pharmacology, and clinical data for currently available BL/BLI treatment options as well as agents in late stage development for CRO harboring various β-lactamases including MBL and OXA-enzymes.
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Affiliation(s)
- Christina Koenig
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, Connecticut, USA
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joseph L Kuti
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, Connecticut, USA
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3
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Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01054-w. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
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Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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4
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Chatupheeraphat C, Peamchai J, Kaewsai N, Anuwongcharoen N, Eiamphungporn W. Enhancing the activity of β-lactamase inhibitory protein-II with cell-penetrating peptide against KPC-2-carrying Klebsiella pneumoniae. PLoS One 2024; 19:e0296727. [PMID: 38277388 PMCID: PMC10817188 DOI: 10.1371/journal.pone.0296727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/16/2023] [Indexed: 01/28/2024] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) is considered a paramount threat due to its rapid spread and high mortality rate. Klebsiella pneumoniae carbapenemases (KPCs), specifically KPC-2, are prevalent enzymes responsible for carbapenem resistance in many countries. While combinations of antibiotics are commonly used, they must be tailored to match the remaining susceptibility of the infecting strains. Therefore, there is a need to develop the β-lactamase inhibitor to effectively address this issue. β-lactamase inhibitor protein (BLIP) and its variants, BLIP-I and BLIP-II, have demonstrated the ability to inhibit class A β-lactamases. In particular, BLIP-II shows strong binding to the KPC-2 carbapenemase, making it a potential candidate for inhibition. To improve the intracellular penetration of BLIP-II, a cell-penetrating peptide (CPP) was employed. In this study, a KRK-rich peptide was introduced at either the N-terminal or C-terminal region of tBLIP-II, excluding the signal sequence of the BLIP-II protein. tBLIP-II, tBLIP-II-CPP, and CPP-BLIP-II were successfully expressed, and the chimeric proteins retained inhibitory activity compared to tBLIP-II alone. It is apparent that homology modeling demonstrated neither the poly-histidine tag nor the CPP interfered with the essential interaction residues of tBLIP-II. Interestingly, BLIP-II-CPP exhibited the highest inhibitory activity, reducing the minimal inhibitory concentration (MIC) of meropenem by 8 folds. Moreover, the combination of tBLIP-CPP with meropenem significantly decreased the viable bacterial cell count compared to the combination of tBLIP-II with meropenem or meropenem alone. These findings suggest that tBLIP-CPP is a promising candidate for restoring carbapenem susceptibility against CRE and provides a valuable therapeutic option for infections caused by CRE.
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Affiliation(s)
- Chawalit Chatupheeraphat
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Jiratchaya Peamchai
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Noramon Kaewsai
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Nuttapat Anuwongcharoen
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Warawan Eiamphungporn
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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5
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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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Ahmad F, Parvaiz N, MacKerell AD, Azam SS. Non-β Lactam Inhibitors of the Serine β-Lactamase blaCTX-M15 in Drug-Resistant Salmonella typhi. J Chem Inf Model 2023; 63:6681-6695. [PMID: 37847018 PMCID: PMC10698858 DOI: 10.1021/acs.jcim.3c00780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Antibiotic resistance by bacterial pathogens against widely used β-lactam drugs is a major concern to public health worldwide, resulting in high healthcare cost. The present study aimed to extend previous research by investigating the potential activity of reported compounds against the S. typhi β-lactamase protein. 74 compounds from computational screening reported in our previous study against β-lactamase CMY-10 were subjected to docking studies against blaCTX-M15. Site-Identification by Ligand Competitive Saturation (SILCS)-Monte Carlo (SILCS-MC) was applied to the top two ligands selected from molecular docking studies to predict and refine their conformations for binding conformations against blaCTX-M15. The SILCS-MC method predicted affinities of -8.6 and -10.7 kcal/mol for Top1 and Top2, respectively, indicating low micromolar binding to the blaCTX-M15 active site. MD simulations initiated from SILCS-MC docked orientations were carried out to better characterize the dynamics and stability of the complexes. Important interactions anchoring the ligand within the active site include pi-pi stacked, amide-pi, and pi-alkyl interactions. Simulations of the Top2-blaCTX-M15 complex exhibited stability associated with a wide range of hydrogen-bond and aromatic interactions between the protein and the ligand. Experimental β-lactamase (BL) activity assays showed that Top1 has 0.1 u/mg BL activity, and Top2 has a BL activity of 0.038 u/mg with a minimum inhibitory concentration of 1 mg/mL. The inhibitors proposed in this study are non-β-lactam-based β-lactamase inhibitors that exhibit the potential to be used in combination with β-lactam antibiotics against multidrug-resistant clinical isolates. Thus, Top1 and Top2 represent lead compounds that increase the efficacy of β-lactam antibiotics with a low dose concentration.
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Affiliation(s)
- Faisal Ahmad
- Both authors contributed equally and can be considered as first author
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad-45320, Pakistan
| | - Nousheen Parvaiz
- Both authors contributed equally and can be considered as first author
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad-45320, Pakistan
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad-45320, Pakistan
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7
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Yan YH, Zhang TT, Li R, Wang SY, Wei LL, Wang XY, Zhu KR, Li SR, Liang GQ, Yang ZB, Yang LL, Qin S, Li GB. Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-β-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding. J Med Chem 2023; 66:13746-13767. [PMID: 37791640 DOI: 10.1021/acs.jmedchem.3c01189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Metallo-β-lactamases (MBLs) are zinc-dependent enzymes capable of hydrolyzing all bicyclic β-lactam antibiotics, posing a great threat to public health. However, there are currently no clinically approved MBL inhibitors. Despite variations in their active sites, MBLs share a common catalytic mechanism with carbapenems, forming similar reaction species and hydrolysates. We here report the development of 2-aminothiazole-4-carboxylic acids (AtCs) as broad-spectrum MBL inhibitors by mimicking the anchor pharmacophore features of carbapenem hydrolysate binding. Several AtCs manifested potent activity against B1, B2, and B3 MBLs. Crystallographic analyses revealed a common binding mode of AtCs with B1, B2, and B3 MBLs, resembling binding observed in the MBL-carbapenem product complexes. AtCs restored Meropenem activity against MBL-producing isolates. In the murine sepsis model, AtCs exhibited favorable synergistic efficacy with Meropenem, along with acceptable pharmacokinetics and safety profiles. This work offers promising lead compounds and a structural basis for the development of potential drug candidates to combat MBL-mediated antimicrobial resistance.
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Affiliation(s)
- Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ting-Ting Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, China
| | - Rong Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Si-Yao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Liu-Liu Wei
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xin-Yue Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Kai-Rong Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shan-Rui Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Guo-Qing Liang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Zeng-Bao Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ling-Ling Yang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, China
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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Thoden JB, Benin BM, Priebe A, Shin WS, Muthyala R, Sham YY, Holden HM. Characterization of a novel inhibitor for the New Delhi metallo-β-lactamase-4: Implications for drug design and combating bacterial drug resistance. J Biol Chem 2023; 299:105135. [PMID: 37549809 PMCID: PMC10514461 DOI: 10.1016/j.jbc.2023.105135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023] Open
Abstract
The bacterial metallo-β-lactamases (MBLs) catalyze the inactivation of β-lactam antibiotics. Identifying novel pharmacophores remains crucial for the clinical development of additional MBL inhibitors. Previously, 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid, hereafter referred to as 1,2-HPT-6-COOH, was reported as a low cytotoxic nanomolar β-lactamase inhibitor of Verona-integron-encoded metallo-β-lactamase 2, capable of rescuing β-lactam antibiotic activity. In this study, we explore its exact mechanism of inhibition and the extent of its activity through structural characterization of its binding to New Delhi metallo-β-lactamase 4 (NDM-4) and its inhibitory activity against both NDM-1 and NDM-4. Of all the structure-validated MBL inhibitors available, 1,2-HPT-6-COOH is the first discovered compound capable of forming an octahedral coordination sphere with Zn2 of the binuclear metal center. This unexpected mechanism of action provides important insight for the further optimization of 1,2-HPT-6-COOH and the identification of additional pharmacophores for MBL inhibition.
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Affiliation(s)
- James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Bogdan M Benin
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Adam Priebe
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Woo Shik Shin
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Ramaiah Muthyala
- Department of Experimental & Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yuk Yin Sham
- Department of Experimental & Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA; Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota, USA.
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA.
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Krco S, Davis SJ, Joshi P, Wilson LA, Monteiro Pedroso M, Douw A, Schofield CJ, Hugenholtz P, Schenk G, Morris MT. Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup-emerging targets to combat antibiotic resistance. Front Chem 2023; 11:1196073. [PMID: 37408556 PMCID: PMC10318434 DOI: 10.3389/fchem.2023.1196073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
β-Lactams are the most widely employed antibiotics in clinical settings due to their broad efficacy and low toxicity. However, since their first use in the 1940s, resistance to β-lactams has proliferated to the point where multi-drug resistant organisms are now one of the greatest threats to global human health. Many bacteria use β-lactamases to inactivate this class of antibiotics via hydrolysis. Although nucleophilic serine-β-lactamases have long been clinically important, most broad-spectrum β-lactamases employ one or two metal ions (likely Zn2+) in catalysis. To date, potent and clinically useful inhibitors of these metallo-β-lactamases (MBLs) have not been available, exacerbating their negative impact on healthcare. MBLs are categorised into three subgroups: B1, B2, and B3 MBLs, depending on their sequence similarities, active site structures, interactions with metal ions, and substrate preferences. The majority of MBLs associated with the spread of antibiotic resistance belong to the B1 subgroup. Most characterized B3 MBLs have been discovered in environmental bacteria, but they are increasingly identified in clinical samples. B3-type MBLs display greater diversity in their active sites than other MBLs. Furthermore, at least one of the known B3-type MBLs is inhibited by the serine-β-lactamase inhibitor clavulanic acid, an observation that may promote the design of derivatives active against a broader range of MBLs. In this Mini Review, recent advances in structure-function relationships of B3-type MBLs will be discussed, with a view to inspiring inhibitor development to combat the growing spread of β-lactam resistance.
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Affiliation(s)
- Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Samuel J. Davis
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Pallav Joshi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Liam A. Wilson
- Chemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Oxford University, Oxford, United Kingdom
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew Douw
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Oxford University, Oxford, United Kingdom
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Marc T. Morris
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
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10
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Ding D, Wang B, Zhang X, Zhang J, Zhang H, Liu X, Gao Z, Yu Z. The spread of antibiotic resistance to humans and potential protection strategies. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114734. [PMID: 36950985 DOI: 10.1016/j.ecoenv.2023.114734] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.
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Affiliation(s)
- Dong Ding
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China; College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Bin Wang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoan Zhang
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junxi Zhang
- NHC Key Laboratory of Birth Defects Prevention & Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Huanhuan Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xinxin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zhan Gao
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Zengli Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China; The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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11
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Oliveira-Tintino CDDM, Tintino SR, Justino de Araújo AC, dos Santos Barbosa CR, Ramos Freitas P, de Araújo Neto JB, Begnini IM, Rebelo RA, da Silva LE, Mireski SL, Nasato MC, Krautler MIL, Barreto HM, Ribeiro-Filho J, de Menezes IRA, Coutinho HDM. Efflux Pump (QacA, QacB, and QacC) and β-Lactamase Inhibitors? An Evaluation of 1,8-Naphthyridines against Staphylococcus aureus Strains. Molecules 2023; 28:molecules28041819. [PMID: 36838807 PMCID: PMC9961278 DOI: 10.3390/molecules28041819] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The bacterial species Staphylococcus aureus presents a variety of resistance mechanisms, among which the expression of β-lactamases and efflux pumps stand out for providing a significant degree of resistance to clinically relevant antibiotics. The 1,8-naphthyridines are nitrogen heterocycles with a broad spectrum of biological activities and, as such, are promising research targets. However, the potential roles of these compounds on bacterial resistance management remain to be better investigated. Therefore, the present study evaluated the antibacterial activity of 1,8-naphthyridine sulfonamides, addressing their ability to act as inhibitors of β-lactamases and efflux pump (QacA/B and QacC) against the strains SA-K4414 and SA-K4100 of S. aureus. All substances were prepared at an initial concentration of 1024 μg/mL, and their minimum inhibitory concentrations (MIC) were determined by the broth microdilution method. Subsequently, their effects on β-lactamase- and efflux pump-mediated antibiotic resistance was evaluated from the reduction of the MIC of ethidium bromide (EtBr) and β-lactam antibiotics, respectively. The 1,8-naphthyridines did not present direct antibacterial activity against the strains SA-K4414 and SA-K4100 of S. aureus. On the other hand, when associated with antibiotics against both strains, the compounds reduced the MIC of EtBr and β-lactam antibiotics, suggesting that they may act by inhibiting β-lactamases and efflux pumps such as QacC and QacA/B. However, further research is required to elucidate the molecular mechanisms underlying these observed effects.
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Affiliation(s)
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology, Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, CE, Brazil
- Correspondence: (S.R.T.); (I.R.A.d.M.)
| | - Ana Carolina Justino de Araújo
- Laboratory of Microbiology and Molecular Biology, Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, CE, Brazil
| | - Cristina Rodrigues dos Santos Barbosa
- Laboratory of Microbiology and Molecular Biology, Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, CE, Brazil
| | - Priscilla Ramos Freitas
- Laboratory of Microbiology and Molecular Biology, Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, CE, Brazil
| | - José Bezerra de Araújo Neto
- Laboratory of Microbiology and Molecular Biology, Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, CE, Brazil
| | - Iêda Maria Begnini
- Department of Chemistry, Regional University of Blumenau (FURB), Itoupava Seca, Blumenau 89030-903, SC, Brazil
| | - Ricardo Andrade Rebelo
- Department of Chemistry, Regional University of Blumenau (FURB), Itoupava Seca, Blumenau 89030-903, SC, Brazil
| | - Luiz Everson da Silva
- Postgraduate Program in Sustainable Territorial Development, Coastal Sector, Federal University of Paraná (UFPR), Curitiba 81531-990, PR, Brazil
| | - Sandro Lucio Mireski
- Department of Chemistry, Regional University of Blumenau (FURB), Itoupava Seca, Blumenau 89030-903, SC, Brazil
| | - Michele Caroline Nasato
- Department of Chemistry, Regional University of Blumenau (FURB), Itoupava Seca, Blumenau 89030-903, SC, Brazil
| | | | | | - Jaime Ribeiro-Filho
- Oswaldo Cruz Foundation (Fiocruz), Fiocruz Ceará, Eusébio 60180-900, CE, Brazil
| | - Irwin Rose Alencar de Menezes
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, CE, Brazil
- Correspondence: (S.R.T.); (I.R.A.d.M.)
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology, Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, CE, Brazil
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12
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Zhou J, Stapleton P, Xavier-Junior FH, Schatzlein A, Haider S, Healy J, Wells G. Triazole-substituted phenylboronic acids as tunable lead inhibitors of KPC-2 antibiotic resistance. Eur J Med Chem 2022; 240:114571. [DOI: 10.1016/j.ejmech.2022.114571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
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13
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Direct Colorimetry of Imipenem Decomposition as a Novel Cost-Effective Method for Detecting Carbapenemase-Producing Enterobacteria. Microbiol Spectr 2022; 10:e0093822. [PMID: 35852323 PMCID: PMC9430894 DOI: 10.1128/spectrum.00938-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In the absence of a molecule that would collectively inhibit both metallo-β-lactamases and serine-reactive carbapenemases, containment of their genes is the main weapon currently available for confronting carbapenem resistance in hospitals. Cost-effective methodologies rapidly detecting carbapenemase-producing enterobacteria (CPE) would facilitate such measures. Herein, a low-cost CPE detection method was developed that was based on the direct colorimetry of the yellow shift caused by the accumulation of diketopiperazines—products of the acid-catalyzed imipenem oligomerization—induced by carbapenemase action on dense solutions of imipenem/cilastatin. The reactions were studied by spectrophotometry in the visible spectrum using preparations of β-lactamases from the four molecular classes. The effects of various buffers on reaction mixtures containing the potent carbapenemases NDM-1 and NMC-A were monitored at 405 nm. Optimal conditions were used for the analysis of cell suspensions, and the assay was evaluated using 66 selected enterobacteria, including 50 CPE as well as 16 carbapenemase-negative strains overexpressing other β-lactamases. The development of the yellow color was specific for carbapenemase-containing enzyme preparations, and the maximum intensity was achieved in acidic or unbuffered conditions in the presence of zinc. When applied on bacterial cell suspensions, the assay could detect CPE with 98% sensitivity and 100% specificity, with results being comparable to those obtained with the Carba NP technique. Direct colorimetry of carbapenemase-induced imipenem decomposition required minimum reagents while exhibiting high accuracy in detecting CPE. Therefore, it should be considered for screening purposes after further clinical evaluation. IMPORTANCE Currently, the spread of multidrug-resistant (MDR) carbapenemase-producing enterobacteria (CPE), mostly in the clinical setting, is among the most pressing public health problems worldwide. In order to effectively control CPE, use of reliable and affordable methods detecting carbapenemase genes or the respective β-lactamases is of vital importance. Herein, we developed a novel method, based on a previously undescribed phenomenon, that can detect CPE with few reagents by direct colorimetry of bacterial suspensions and imipenem/cilastatin mixtures.
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14
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Iqbal Z, Sun J, Yang H, Ji J, He L, Zhai L, Ji J, Zhou P, Tang D, Mu Y, Wang L, Yang Z. Recent Developments to Cope the Antibacterial Resistance via β-Lactamase Inhibition. Molecules 2022; 27:3832. [PMID: 35744953 PMCID: PMC9227086 DOI: 10.3390/molecules27123832] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 12/01/2022] Open
Abstract
Antibacterial resistance towards the β-lactam (BL) drugs is now ubiquitous, and there is a major global health concern associated with the emergence of new β-lactamases (BLAs) as the primary cause of resistance. In addition to the development of new antibacterial drugs, β-lactamase inhibition is an alternative modality that can be implemented to tackle this resistance channel. This strategy has successfully revitalized the efficacy of a number of otherwise obsolete BLs since the discovery of the first β-lactamase inhibitor (BLI), clavulanic acid. Over the years, β-lactamase inhibition research has grown, leading to the introduction of new synthetic inhibitors, and a few are currently in clinical trials. Of note, the 1, 6-diazabicyclo [3,2,1]octan-7-one (DBO) scaffold gained the attention of researchers around the world, which finally culminated in the approval of two BLIs, avibactam and relebactam, which can successfully inhibit Ambler class A, C, and D β-lactamases. Boronic acids have shown promise in coping with Ambler class B β-lactamases in recent research, in addition to classes A, C, and D with the clinical use of vaborbactam. This review focuses on the further developments in the synthetic strategies using DBO as well as boronic acid derivatives. In addition, various other potential serine- and metallo- β-lactamases inhibitors that have been developed in last few years are discussed briefly as well. Furthermore, binding interactions of the representative inhibitors have been discussed based on the crystal structure data of inhibitor-enzyme complex, published in the literature.
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Affiliation(s)
- Zafar Iqbal
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan 750002, China; (H.Y.); (J.J.); (L.H.); (L.Z.); (J.J.); (P.Z.); (D.T.); (Y.M.); (L.W.)
| | - Jian Sun
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan 750002, China; (H.Y.); (J.J.); (L.H.); (L.Z.); (J.J.); (P.Z.); (D.T.); (Y.M.); (L.W.)
| | | | | | | | | | | | | | | | | | | | - Zhixiang Yang
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan 750002, China; (H.Y.); (J.J.); (L.H.); (L.Z.); (J.J.); (P.Z.); (D.T.); (Y.M.); (L.W.)
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15
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Penicillanic Acid Sulfones Inactivate the Extended-Spectrum β-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: an Alternative Mechanism of β-Lactamase Inhibition. mBio 2022; 13:e0179321. [PMID: 35612361 PMCID: PMC9239225 DOI: 10.1128/mbio.01793-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
β-Lactamases hydrolyze β-lactam antibiotics and are major determinants of antibiotic resistance in Gram-negative pathogens. Enmetazobactam (formerly AAI101) and tazobactam are penicillanic acid sulfone (PAS) β-lactamase inhibitors that differ by an additional methyl group on the triazole ring of enmetazobactam, rendering it zwitterionic. In this study, ultrahigh-resolution X-ray crystal structures and mass spectrometry revealed the mechanism of PAS inhibition of CTX-M-15, an extended-spectrum β-lactamase (ESBL) globally disseminated among Enterobacterales. CTX-M-15 crystals grown in the presence of enmetazobactam or tazobactam revealed loss of the Ser70 hydroxyl group and formation of a lysinoalanine cross-link between Lys73 and Ser70, two residues critical for catalysis. Moreover, the residue at position 70 undergoes epimerization, resulting in formation of a d-amino acid. Cocrystallization of enmetazobactam or tazobactam with CTX-M-15 with a Glu166Gln mutant revealed the same cross-link, indicating that this modification is not dependent on Glu166-catalyzed deacylation of the PAS-acylenzyme. A cocrystal structure of enmetazobactam with CTX-M-15 with a Lys73Ala mutation indicates that epimerization can occur without cross-link formation and positions the Ser70 Cβ closer to Lys73, likely facilitating formation of the Ser70-Lys73 cross-link. A crystal structure of a tazobactam-derived imine intermediate covalently linked to Ser70, obtained after 30 min of exposure of CTX-M-15 crystals to tazobactam, supports formation of an initial acylenzyme by PAS inhibitors on reaction with CTX-M-15. These data rationalize earlier results showing CTX-M-15 deactivation by PAS inhibitors to involve loss of protein mass, and they identify a distinct mechanism of β-lactamase inhibition by these agents.
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16
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The development of New Delhi metallo-β-lactamase-1 inhibitors since 2018. Microbiol Res 2022; 261:127079. [DOI: 10.1016/j.micres.2022.127079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022]
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17
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Messner K, Vuong B, Tranmer GK. The Boron Advantage: The Evolution and Diversification of Boron’s Applications in Medicinal Chemistry. Pharmaceuticals (Basel) 2022; 15:ph15030264. [PMID: 35337063 PMCID: PMC8948683 DOI: 10.3390/ph15030264] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 12/13/2022] Open
Abstract
In this review, the history of boron’s early use in drugs, and the history of the use of boron functional groups in medicinal chemistry applications are discussed. This includes diazaborines, boronic acids, benzoxaboroles, boron clusters, and carboranes. Furthermore, critical developments from these functional groups are highlighted along with recent developments, which exemplify potential prospects. Lastly, the application of boron in the form of a prodrug, softdrug, and as a nanocarrier are discussed to showcase boron’s emergence into new and exciting fields. Overall, we emphasize the evolution of organoboron therapeutic agents as privileged structures in medicinal chemistry and outline the impact that boron has had on drug discovery and development.
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Affiliation(s)
- Katia Messner
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
| | - Billy Vuong
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
| | - Geoffrey K. Tranmer
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
- Department of Chemistry, Faculty of Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
- Correspondence:
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18
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Cui CY, Chen Q, He Q, Chen C, Zhang RM, Feng Y, Sun J. Transferability of tigecycline resistance: Characterization of the expanding Tet(X) family. WIREs Mech Dis 2022; 14:e1538. [PMID: 35023325 DOI: 10.1002/wsbm.1538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023]
Abstract
Tetracycline and its derivative tigecycline are clinical options against Gram-negative bacterial infections. The emergence of mobile Tet(X) enzymes that destruct tetracycline-type antibiotics is posing a big challenge to antibacterial therapy and food/environmental securities. Here, we present an update on a growing number of Tet(X) variants. We describe structure and action of Tet(X) enzyme, and discuss the evolutional origin. In addition, potential Tet(X) inhibitors are given. This mini-review might benefit better understanding of Tet(X)-mediated tigecycline resistance. This article is categorized under: Infectious Diseases > Genetics/Genomics/Epigenetics Infectious Diseases > Environmental Factors Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Chao-Yue Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qiwei Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China.,Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qian He
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Chong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Rong-Min Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Youjun Feng
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
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19
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Ming W, Soor HS, Liu X, Trofimova A, Yudin AK, Marder TB. α-Aminoboronates: recent advances in their preparation and synthetic applications. Chem Soc Rev 2021; 50:12151-12188. [PMID: 34585200 DOI: 10.1039/d1cs00423a] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
α-Aminoboronic acids and their derivatives are useful as bioactive agents. Thus far, three compounds containing an α-aminoboronate motif have been approved by the Food and Drug Administration (FDA) as protease inhibitors, and more are currently undergoing clinical trials. In addition, α-aminoboronic acids and their derivatives have found applications in organic synthesis, e.g. as α-aminomethylation reagents for the synthesis of chiral nitrogen-containing molecules, as nucleophiles for preparing valuable vicinal amino alcohols, and as bis-nucleophiles in the construction of valuable small molecule scaffolds. This review summarizes new methodology for the preparation of α-aminoboronates, including highlights of asymmetric synthetic methods and mechanistic explanations of reactivity. Applications of α-aminoboronates as versatile synthetic building blocks are also discussed.
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Affiliation(s)
- Wenbo Ming
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Harjeet S Soor
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada.
| | - Xiaocui Liu
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Alina Trofimova
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada.
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada.
| | - Todd B Marder
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
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20
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Yahiaoui S, Voos K, Haupenthal J, Wichelhaus TA, Frank D, Weizel L, Rotter M, Brunst S, Kramer JS, Proschak E, Ducho C, Hirsch AKH. N-Aryl mercaptoacetamides as potential multi-target inhibitors of metallo-β-lactamases (MBLs) and the virulence factor LasB from Pseudomonas aeruginosa. RSC Med Chem 2021; 12:1698-1708. [PMID: 34778771 PMCID: PMC8528214 DOI: 10.1039/d1md00187f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/23/2021] [Indexed: 12/18/2022] Open
Abstract
Increasing antimicrobial resistance is evolving to be one of the major threats to public health. To reduce the selection pressure and thus to avoid a fast development of resistance, novel approaches aim to target bacterial virulence instead of growth. Another strategy is to restore the activity of antibiotics already in clinical use. This can be achieved by the inhibition of resistance factors such as metallo-β-lactamases (MBLs). Since MBLs can cleave almost all β-lactam antibiotics, including the “last resort” carbapenems, their inhibition is of utmost importance. Here, we report on the synthesis and in vitro evaluation of N-aryl mercaptoacetamides as inhibitors of both clinically relevant MBLs and the virulence factor LasB from Pseudomonas aeruginosa. All tested N-aryl mercaptoacetamides showed low micromolar to submicromolar activities on the tested enzymes IMP-7, NDM-1 and VIM-1. The two most promising compounds were further examined in NDM-1 expressing Klebsiella pneumoniae isolates, where they restored the full activity of imipenem. Together with their LasB-inhibitory activity in the micromolar range, this class of compounds can now serve as a starting point for a multi-target inhibitor approach against both bacterial resistance and virulence, which is unprecedented in antibacterial drug discovery. Simultaneous inhibition of metallo-β-lactamases (MBLs) and virulence factors such as LasB from Pseudomonas aeruginosa offers a new approach to combat antibiotic-resistant pathogens.![]()
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Affiliation(s)
- Samir Yahiaoui
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Katrin Voos
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt Paul-Ehrlich-Straße 40 60596 Frankfurt Germany
| | - Denia Frank
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt Paul-Ehrlich-Straße 40 60596 Frankfurt Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Marco Rotter
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University Campus Building E8 1 66123 Saarbrücken Germany
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21
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Shurina BA, Page RC. Structural Comparisons of Cefotaximase (CTX-M-ase) Sub Family 1. Front Microbiol 2021; 12:688509. [PMID: 34504475 PMCID: PMC8421805 DOI: 10.3389/fmicb.2021.688509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022] Open
Abstract
The cefotaximase or CTX-M, family of serine-β-lactamases represents a significant clinical concern due to the ability for these enzymes to confer resistance to a broad array of β-lactam antibiotics an inhibitors. This behavior lends CTX-M-ases to be classified as extended spectrum β-lactamases (ESBL). Across the family of CTX-M-ases most closely related to CTX-M-1, the structures of CTX-M-15 with a library of different ligands have been solved and serve as the basis of comparison within this review. Herein we focus on the structural changes apparent in structures of CTX-M-15 in complex with diazabicyclooctane (DABCO) and boronic acid transition state analog inhibitors. Interactions between a positive surface patch near the active site and complementary functional groups of the bound inhibitor play key roles in the dictating the conformations of active site residues. The insights provided by analyzing structures of CTX-M-15 in complex with DABCO and boronic acid transition state analog inhibitors and analyzing existing structures of CTX-M-64 offer opportunities to move closer to making predictions as to how CTX-M-ases may interact with potential drug candidates, setting the stage for the further development of new antibiotics and β-lactamase inhibitors.
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Affiliation(s)
- Ben A Shurina
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, United States
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, United States.,Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH, United States
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22
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Charzewski Ł, Krzyśko KA, Lesyng B. Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations. Front Mol Biosci 2021; 8:633181. [PMID: 34434961 PMCID: PMC8380965 DOI: 10.3389/fmolb.2021.633181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Recently, molecular covalent docking has been extensively developed to design new classes of inhibitors that form chemical bonds with their biological targets. This strategy for the design of such inhibitors, in particular boron-based inhibitors, holds great promise for the vast family of β-lactamases produced, inter alia, by Gram-negative antibiotic-resistant bacteria. However, the description of covalent docking processes requires a quantum-mechanical approach, and so far, only a few studies of this type have been presented. This study accurately describes the covalent docking process between two model inhibitors - representing two large families of inhibitors based on boronic-acid and bicyclic boronate scaffolds, and three β-lactamases which belong to the A, C, and D classes. Molecular fragments containing boron can be converted from a neutral, trigonal, planar state with sp2 hybridization to the anionic, tetrahedral sp3 state in a process sometimes referred to as morphing. This study applies multi-scale modeling methods, in particular, the hybrid QM/MM approach which has predictive power reaching well beyond conventional molecular modeling. Time-dependent QM/MM simulations indicated several structural changes and geometric preferences, ultimately leading to covalent docking processes. With current computing technologies, this approach is not computationally expensive, can be used in standard molecular modeling and molecular design works, and can effectively support experimental research which should allow for a detailed understanding of complex processes important to molecular medicine. In particular, it can support the rational design of covalent boron-based inhibitors for β-lactamases as well as for many other enzyme systems of clinical relevance, including SARS-CoV-2 proteins.
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Affiliation(s)
| | | | - Bogdan Lesyng
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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23
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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24
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Egorov AM, Ulyashova MM, Rubtsova MY. Inhibitors of β-Lactamases. New Life of β-Lactam Antibiotics. BIOCHEMISTRY (MOSCOW) 2021; 85:1292-1309. [PMID: 33280574 DOI: 10.1134/s0006297920110024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
β-Lactam antibiotics account for about 60% of all produced antibiotics. Due to a high activity and minimal side effects, they are the most commonly used class of antibacterial drugs for the treatment of various infectious diseases of humans and animals, including severe hospital infections. However, the emergence of bacteria resistant to β-lactams has led to the clinical inefficiency of these antibiotics, and as a result, their use in medicine has been limited. The search for new effective ways for overcoming the resistance to β-lactam antibiotics is an essential task. The major mechanism of bacterial resistance is the synthesis of β-lactamases (BLs) that break the antibiotic β-lactam ring. Here, we review specific inhibitors of serine β-lactamases and metallo-β-lactamases and discuss approaches for creating new inhibitors that would prolong the "life" of β-lactams.
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Affiliation(s)
- A M Egorov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - M M Ulyashova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - M Yu Rubtsova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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25
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Tehrani KHME, Wade N, Mashayekhi V, Brüchle NC, Jespers W, Voskuil K, Pesce D, van Haren MJ, van Westen GJP, Martin NI. Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-β-Lactamases. J Med Chem 2021; 64:9141-9151. [PMID: 34182755 PMCID: PMC8273888 DOI: 10.1021/acs.jmedchem.1c00362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In an attempt to exploit the hydrolytic mechanism by which β-lactamases degrade cephalosporins, we designed and synthesized a series of novel cephalosporin prodrugs aimed at delivering thiol-based inhibitors of metallo-β-lactamases (MBLs) in a spatiotemporally controlled fashion. While enzymatic hydrolysis of the β-lactam ring was observed, it was not accompanied by inhibitor release. Nonetheless, the cephalosporin prodrugs, especially thiomandelic acid conjugate (8), demonstrated potent inhibition of IMP-type MBLs. In addition, conjugate 8 was also found to greatly reduce the minimum inhibitory concentration of meropenem against IMP-producing bacteria. The results of kinetic experiments indicate that these prodrugs inhibit IMP-type MBLs by acting as slowly turned-over substrates. Structure-activity relationship studies revealed that both phenyl and carboxyl moieties of 8 are crucial for its potency. Furthermore, modeling studies indicate that productive interactions of the thiomandelic acid moiety of 8 with Trp28 within the IMP active site may contribute to its potency and selectivity.
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Affiliation(s)
- Kamaleddin H M E Tehrani
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Nicola Wade
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Vida Mashayekhi
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nora C Brüchle
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Willem Jespers
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.,Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Koen Voskuil
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Diego Pesce
- Laboratory of Genetics, Wageningen University and Research, 6700 AA Wageningen, The Netherlands.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthijs J van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Gerard J P van Westen
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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26
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Luci G, Mattioli F, Falcone M, Di Paolo A. Pharmacokinetics of Non-β-Lactam β-Lactamase Inhibitors. Antibiotics (Basel) 2021; 10:769. [PMID: 34202609 PMCID: PMC8300739 DOI: 10.3390/antibiotics10070769] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022] Open
Abstract
The growing emergence of drug-resistant bacterial strains is an issue to treat severe infections, and many efforts have identified new pharmacological agents. The inhibitors of β-lactamases (BLI) have gained a prominent role in the safeguard of beta-lactams. In the last years, new β-lactam-BLI combinations have been registered or are still under clinical evaluation, demonstrating their effectiveness to treat complicated infections. It is also noteworthy that the pharmacokinetics of BLIs partly matches that of β-lactams companions, meaning that some clinical situations, as well as renal impairment and renal replacement therapies, may alter the disposition of both drugs. Common pharmacokinetic characteristics, linear pharmacokinetics across a wide range of doses, and known pharmacokinetic/pharmacodynamic parameters may guide modifications of dosing regimens for both β-lactams and BLIs. However, comorbidities (i.e., burns, diabetes, cancer) and severe changes in individual pathological conditions (i.e., acute renal impairment, sepsis) could make dose adaptation difficult, because the impact of those factors on BLI pharmacokinetics is partly known. Therapeutic drug monitoring protocols may overcome those issues and offer strategies to personalize drug doses in the intensive care setting. Further prospective clinical trials are warranted to improve the use of BLIs and their β-lactam companions in severe and complicated infections.
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Affiliation(s)
- Giacomo Luci
- Department of Clinical and Experimental Medicine, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (G.L.); (M.F.)
| | - Francesca Mattioli
- Department of Internal Medicine, Pharmacology & Toxicology Unit, University of Genoa, 16100 Genoa, Italy;
| | - Marco Falcone
- Department of Clinical and Experimental Medicine, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (G.L.); (M.F.)
| | - Antonello Di Paolo
- Department of Clinical and Experimental Medicine, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (G.L.); (M.F.)
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27
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Farley AM, Ermolovich Y, Calvopiña K, Rabe P, Panduwawala T, Brem J, Björkling F, Schofield CJ. Structural Basis of Metallo-β-lactamase Inhibition by N-Sulfamoylpyrrole-2-carboxylates. ACS Infect Dis 2021; 7:1809-1817. [PMID: 34003651 PMCID: PMC8205225 DOI: 10.1021/acsinfecdis.1c00104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Indexed: 12/21/2022]
Abstract
Metallo-β-lactamases (MBLs) can efficiently catalyze the hydrolysis of all classes of β-lactam antibiotics except monobactams. While serine-β-lactamase (SBL) inhibitors (e.g., clavulanic acid, avibactam) are established for clinical use, no such MBL inhibitors are available. We report on the synthesis and mechanism of inhibition of N-sulfamoylpyrrole-2-carboxylates (NSPCs) which are potent inhibitors of clinically relevant B1 subclass MBLs, including NDM-1. Crystallography reveals that the N-sulfamoyl NH2 group displaces the dizinc bridging hydroxide/water of the B1 MBLs. Comparison of crystal structures of an NSPC and taniborbactam (VRNX-5133), presently in Phase III clinical trials, shows similar binding modes for the NSPC and the cyclic boronate ring systems. The presence of an NSPC restores meropenem efficacy in clinically derived E. coli and K. pneumoniae blaNDM-1. The results support the potential of NSPCs and related compounds as efficient MBL inhibitors, though further optimization is required for their clinical development.
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Affiliation(s)
- Alistair
J. M. Farley
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yuri Ermolovich
- Department
of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Karina Calvopiña
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Patrick Rabe
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tharindi Panduwawala
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Fredrik Björkling
- Department
of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Christopher J. Schofield
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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28
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Discovery of 3-aryl substituted benzoxaboroles as broad-spectrum inhibitors of serine- and metallo-β-lactamases. Bioorg Med Chem Lett 2021; 41:127956. [DOI: 10.1016/j.bmcl.2021.127956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/26/2021] [Accepted: 03/07/2021] [Indexed: 11/22/2022]
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29
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Antimicrobial Resistance Conferred by OXA-48 β-Lactamases: Towards a Detailed Mechanistic Understanding. Antimicrob Agents Chemother 2021; 65:AAC.00184-21. [PMID: 33753332 DOI: 10.1128/aac.00184-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OXA-48-type β-lactamases are now routinely encountered in bacterial infections caused by carbapenem-resistant Enterobacterales These enzymes are of high and growing clinical significance due to the importance of carbapenems in treatment of health care-associated infections by Gram-negative bacteria, the wide and increasing dissemination of OXA-48 enzymes on plasmids, and the challenges posed by their detection. OXA-48 confers resistance to penicillin (which is efficiently hydrolyzed) and carbapenem antibiotics (which is more slowly broken down). In addition to the parent enzyme, a growing array of variants of OXA-48 is now emerging. The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins. The growth in importance and diversity of the OXA-48 group has motivated increasing numbers of studies that aim to elucidate the relationship between structure and specificity and establish the mechanistic basis for β-lactam turnover in this enzyme family. In this review, we collate recently published structural, kinetic, and mechanistic information on the interactions between clinically relevant β-lactam antibiotics and inhibitors and OXA-48 β-lactamases. Collectively, these studies are starting to form a detailed picture of the underlying bases for the differences in β-lactam specificity between OXA-48 variants and the consequent differences in resistance phenotype. We focus specifically on aspects of carbapenemase and cephalosporinase activities of OXA-48 β-lactamases and discuss β-lactamase inhibitor development in this context. Throughout the review, we also outline key open research questions for future investigation.
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30
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Krivitskaya AV, Khrenova MG. Boronic Acids as Prospective Inhibitors of Metallo-β-Lactamases: Efficient Chemical Reaction in the Enzymatic Active Site Revealed by Molecular Modeling. Molecules 2021; 26:2026. [PMID: 33918209 PMCID: PMC8038151 DOI: 10.3390/molecules26072026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/08/2023] Open
Abstract
Boronic acids are prospective compounds in inhibition of metallo-β-lactamases as they form covalent adducts with the catalytic hydroxide anion in the enzymatic active site upon binding. We compare this chemical reaction in the active site of the New Delhi metallo-β-lactamase (NDM-1) with the hydrolysis of the antibacterial drug imipenem. The nucleophilic attack occurs with the energy barrier of 14 kcal/mol for imipenem and simultaneously upon binding a boronic acid inhibitor. A boron atom of an inhibitor exhibits stronger electrophilic properties than the carbonyl carbon atom of imipenem in a solution that is quantified by atomic Fukui indices. Upon forming the prereaction complex between NDM-1 and inhibitor, the lone electron pair of the nucleophile interacts with the vacant p-orbital of boron that facilitates the chemical reaction. We analyze a set of boronic acid compounds with the benzo[b]thiophene core complexed with the NDM-1 and propose quantitative structure-sroperty relationship (QSPR) equations that can predict IC50 values from the calculated descriptors of electron density. These relations are applied to classify other boronic acids with the same core found in the database of chemical compounds, PubChem, and proposed ourselves. We demonstrate that the IC50 values for all considered benzo[b]thiophene-containing boronic acid inhibitors are 30-70 μM.
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Affiliation(s)
- Alexandra V. Krivitskaya
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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31
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Romero E, Oueslati S, Benchekroun M, D'Hollander ACA, Ventre S, Vijayakumar K, Minard C, Exilie C, Tlili L, Retailleau P, Zavala A, Elisée E, Selwa E, Nguyen LA, Pruvost A, Naas T, Iorga BI, Dodd RH, Cariou K. Azetidinimines as a novel series of non-covalent broad-spectrum inhibitors of β-lactamases with submicromolar activities against carbapenemases KPC-2 (class A), NDM-1 (class B) and OXA-48 (class D). Eur J Med Chem 2021; 219:113418. [PMID: 33862516 DOI: 10.1016/j.ejmech.2021.113418] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022]
Abstract
The occurrence of resistances in Gram negative bacteria is steadily increasing to reach extremely worrying levels and one of the main causes of resistance is the massive spread of very efficient β-lactamases which render most β-lactam antibiotics useless. Herein, we report the development of a series of imino-analogues of β-lactams (namely azetidinimines) as efficient non-covalent inhibitors of β-lactamases. Despite the structural and mechanistic differences between serine-β-lactamases KPC-2 and OXA-48 and metallo-β-lactamase NDM-1, all three enzymes can be inhibited at a submicromolar level by compound 7dfm, which can also repotentiate imipenem against a resistant strain of Escherichia coli expressing NDM-1. We show that 7dfm can efficiently inhibit not only the three main clinically-relevant carbapenemases of Ambler classes A (KPC-2), B (NDM-1) and D (OXA-48) with Ki's below 0.3 μM, but also the cephalosporinase CMY-2 (class C, 86% inhibition at 10 μM). Our results pave the way for the development of a new structurally original family of non-covalent broad-spectrum inhibitors of β-lactamases.
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Affiliation(s)
- Eugénie Romero
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Saoussen Oueslati
- U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Mohamed Benchekroun
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Agathe C A D'Hollander
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Sandrine Ventre
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Kamsana Vijayakumar
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Corinne Minard
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Cynthia Exilie
- U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Linda Tlili
- U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Pascal Retailleau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Agustin Zavala
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France; U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Eddy Elisée
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Edithe Selwa
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Laetitia A Nguyen
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour La Santé, Gif-sur-Yvette, France
| | - Alain Pruvost
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour La Santé, Gif-sur-Yvette, France
| | - Thierry Naas
- U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; EERA Unit "Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-AP-HP-Université Paris-Saclay, Paris, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France.
| | - Robert H Dodd
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Kevin Cariou
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France.
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32
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Aertker KMJ, Chan HTH, Lohans CT, Schofield CJ. Analysis of β-lactone formation by clinically observed carbapenemases informs on a novel antibiotic resistance mechanism. J Biol Chem 2020; 295:16604-16613. [PMID: 32963107 PMCID: PMC7864059 DOI: 10.1074/jbc.ra120.014607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/07/2020] [Indexed: 01/18/2023] Open
Abstract
An important mechanism of resistance to β-lactam antibiotics is via their β-lactamase-catalyzed hydrolysis. Recent work has shown that, in addition to the established hydrolysis products, the reaction of the class D nucleophilic serine β-lactamases (SBLs) with carbapenems also produces β-lactones. We report studies on the factors determining β-lactone formation by class D SBLs. We show that variations in hydrophobic residues at the active site of class D SBLs (i.e. Trp105, Val120, and Leu158, using OXA-48 numbering) impact on the relative levels of β-lactones and hydrolysis products formed. Some variants, i.e. the OXA-48 V120L and OXA-23 V128L variants, catalyze increased β-lactone formation compared with the WT enzymes. The results of kinetic and product studies reveal that variations of residues other than those directly involved in catalysis, including those arising from clinically observed mutations, can alter the reaction outcome of class D SBL catalysis. NMR studies show that some class D SBL variants catalyze formation of β-lactones from all clinically relevant carbapenems regardless of the presence or absence of a 1β-methyl substituent. Analysis of reported crystal structures for carbapenem-derived acyl-enzyme complexes reveals preferred conformations for hydrolysis and β-lactone formation. The observation of increased β-lactone formation by class D SBL variants, including the clinically observed carbapenemase OXA-48 V120L, supports the proposal that class D SBL-catalyzed rearrangement of β-lactams to β-lactones is important as a resistance mechanism.
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Affiliation(s)
| | - H T Henry Chan
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom; Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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Piccirilli A, Segatore B, Brisdelli F, Amicosante G, Perilli M. Potent inhibitory activity of taniborbactam towards NDM-1 and NDM-1 Q119X mutants, and in vitro activity of cefepime/taniborbactam against MBLs producing Enterobacterales. Int J Antimicrob Agents 2020; 57:106228. [PMID: 33246038 DOI: 10.1016/j.ijantimicag.2020.106228] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/26/2020] [Accepted: 11/07/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE This study aimed to investigate the in vitro activity of taniborbactam (VNRX-5133), a novel broad-spectrum bicyclic boronate, against NDM-1 and Q119E, Q119K, Q119C, Q119F, Q119V, and Q119Y NDM-1 variants, which showed an increased activity towards some β-lactams, including cefepime. METHODS Inhibition kinetic assays were spectrophotometrically performed using cefepime (50 μM) as the reporter substrate and 80 nM of each enzyme. Taniborbactam behaves as a competitive inhibitor towards NDM-1 and NDM-1 Q119 variants with lower Ki values (range 3-16 nM). The phenotypic profile was assessed in both Enterobacterales clinical isolates and engineered Escherichia coli BL21(DE3) strains by conventional broth microdilution procedures according to the Clinical and Laboratory Standards Institute (CLSI). RESULTS Taniborbactam at a fixed concentration of 4 mg/L was able to restore activity of cefepime in 24 of 26 Enterobacterales clinical isolates harbouring metallo-β-lactamases with MIC50/MIC90 values of 14 mg/L. Cefepime MICs were drastically reduced in all clinical isolates and in NDM-1 and Q119X producing Escherichia coli BL21(DE3). Taniborbactam was unable to restore susceptibility to cefepime in two IMP variants producing clinical isolates. CONCLUSION The inhibition level of NDM enzymes provided by taniborbactam protects the antibacterial activity of cefepime from this important metallo-β-lactamase.
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Affiliation(s)
- Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Bernardetta Segatore
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Fabrizia Brisdelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
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Boyd SE, Livermore DM, Hooper DC, Hope WW. Metallo-β-Lactamases: Structure, Function, Epidemiology, Treatment Options, and the Development Pipeline. Antimicrob Agents Chemother 2020; 64:e00397-20. [PMID: 32690645 PMCID: PMC7508574 DOI: 10.1128/aac.00397-20] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Modern medicine is threatened by the global rise of antibiotic resistance, especially among Gram-negative bacteria. Metallo-β-lactamase (MBL) enzymes are a particular concern and are increasingly disseminated worldwide, though particularly in Asia. Many MBL producers have multiple further drug resistances, leaving few obvious treatment options. Nonetheless, and more encouragingly, MBLs may be less effective agents of carbapenem resistance in vivo, under zinc limitation, than in vitro Owing to their unique structure and function and their diversity, MBLs pose a particular challenge for drug development. They evade all recently licensed β-lactam-β-lactamase inhibitor combinations, although several stable agents and inhibitor combinations are at various stages in the development pipeline. These potential therapies, along with the epidemiology of producers and current treatment options, are the focus of this review.
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Affiliation(s)
- Sara E Boyd
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, United Kingdom
| | - David M Livermore
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - William W Hope
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
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Selleck C, Pedroso MM, Wilson L, Krco S, Knaven EG, Miraula M, Mitić N, Larrabee JA, Brück T, Clark A, Guddat LW, Schenk G. Structure and mechanism of potent bifunctional β-lactam- and homoserine lactone-degrading enzymes from marine microorganisms. Sci Rep 2020; 10:12882. [PMID: 32732933 PMCID: PMC7392888 DOI: 10.1038/s41598-020-68612-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/26/2020] [Indexed: 11/11/2022] Open
Abstract
Genes that confer antibiotic resistance can rapidly be disseminated from one microorganism to another by mobile genetic elements, thus transferring resistance to previously susceptible bacterial strains. The misuse of antibiotics in health care and agriculture has provided a powerful evolutionary pressure to accelerate the spread of resistance genes, including those encoding β-lactamases. These are enzymes that are highly efficient in inactivating most of the commonly used β-lactam antibiotics. However, genes that confer antibiotic resistance are not only associated with pathogenic microorganisms, but are also found in non-pathogenic (i.e. environmental) microorganisms. Two recent examples are metal-dependent β-lactamases (MBLs) from the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans. Previous studies have demonstrated that their β-lactamase activity is comparable to those of well-known MBLs from pathogenic sources (e.g. NDM-1, AIM-1) but that they also possess efficient lactonase activity, an activity associated with quorum sensing. Here, we probed the structure and mechanism of these two enzymes using crystallographic, spectroscopic and fast kinetics techniques. Despite highly conserved active sites both enzymes demonstrate significant variations in their reaction mechanisms, highlighting both the extraordinary ability of MBLs to adapt to changing environmental conditions and the rather promiscuous acceptance of diverse substrates by these enzymes.
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Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Liam Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Esmée Gianna Knaven
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Manfredi Miraula
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Department of Chemistry, Maynooth University, Maynooth, County Kildare, Ireland
| | - Nataša Mitić
- Department of Chemistry, Maynooth University, Maynooth, County Kildare, Ireland
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748, Garching, Germany
| | - Alice Clark
- Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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36
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Jalde SS, Choi HK. Recent advances in the development of β-lactamase inhibitors. J Microbiol 2020; 58:633-647. [PMID: 32720096 DOI: 10.1007/s12275-020-0285-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023]
Abstract
β-Lactam antibiotics are the most commonly prescribed antibiotics worldwide; however, antimicrobial resistance (AMR) is a global challenge. The β-lactam resistance in Gram-negative bacteria is due to the production of β-lactamases, including extended-spectrum β-lactamases, metallo-β-lactamases, and carbapenem-hydrolyzing class D β-lactamases. To restore the efficacy of BLAs, the most successful strategy is to use them in combination with β-lactamase inhibitors (BLI). Here we review the medically relevant β-lactamase families and penicillins, diazabicyclooctanes, boronic acids, and novel chemical scaffold-based BLIs, in particular approved and under clinical development.
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Affiliation(s)
- Shivakumar S Jalde
- Department of Medicinal Chemistry, Jungwon University, Goesan, 28420, Republic of Korea
| | - Hyun Kyung Choi
- Department of Medicinal Chemistry, Jungwon University, Goesan, 28420, Republic of Korea.
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37
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Chen AY, Thomas CA, Thomas PW, Yang K, Cheng Z, Fast W, Crowder MW, Cohen SM. Iminodiacetic Acid as a Novel Metal-Binding Pharmacophore for New Delhi Metallo-β-lactamase Inhibitor Development. ChemMedChem 2020; 15:1272-1282. [PMID: 32315115 PMCID: PMC7434514 DOI: 10.1002/cmdc.202000123] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/20/2020] [Indexed: 12/12/2022]
Abstract
The fungal natural product aspergillomarasmine A (AMA) has been identified as a noncompetitive inhibitor of New Delhi metallo-β-lactamase-1 (NDM-1) that inhibits by removing ZnII from the active-site. The nonselective metal-chelating properties and difficult synthesis and derivatization of AMA have hindered the development of this scaffold into a potent and selective inhibitor of NDM-1. Iminodiacetic acid (IDA) has been identified as the metal-binding pharmacophore (MBP) core of AMA that can be leveraged for inhibitor development. Herein, we report the use of IDA for fragment-based drug discovery (FBDD) of NDM-1 inhibitors. IDA (IC50 =120 μM) was developed into inhibitor 23 f (IC50 =8.6 μM, Ki =2.6 μM), which formed a ternary complex with NDM-1, as evidenced by protein thermal-shift and native-state electrospray ionization mass spectrometry (ESI-MS) experiments. Combining mechanistic analysis with inhibitor derivatization, the use of IDA as an alternative AMA scaffold for NDM-1 inhibitor development is detailed.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Austin, TX 78712, USA
| | - Kundi Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Austin, TX 78712, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
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38
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Yu P, Yang JN, Yan JW, Meng ZZ, Hong WD, Roberts AP, Ward SA, Zhang L, Li S. A novel fluorescent probe for the detection of AmpC beta-lactamase and the application in screening beta-lactamase inhibitors. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 234:118257. [PMID: 32208355 DOI: 10.1016/j.saa.2020.118257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/01/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
The rapid detection of β-lactamases (Blas) and effective screening of Bla inhibitors are critically important and urgent for solving antibiotic resistance and improving precision medicine. Here a novel fluorescent probe CDC-559 was designed and synthesized, which can be used for the selective and direct detection of AmpC Blas. More importantly, it can realize screening the Bla inhibitors with sulbactam sodium and tazobactam as model compounds, and the half-maximal inhibitory concentration are 0.279 μM and 0.053 μM, respectively. CDC-559 can be applied not only to examine the resistance of bacterial strains, but also to categorize its mode of action specifically, which is consistent with the essential result of the Blas. The research suggests that CDC-559 probe has tremendous potential in the rapid detection of AmpC Blas as well as the strains with AmpC-encoded gene, which is instructive in promoting better antibiotic stewardship practices and developments.
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Affiliation(s)
- Pan Yu
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jia-Ning Yang
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jin-Wu Yan
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Zhi-Zhong Meng
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - W David Hong
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Adam P Roberts
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Stephen A Ward
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Lei Zhang
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Engineering and Technological Centre for Biopharmaceuticals, South China University of Technology, Guangzhou 510006, PR China.
| | - Shan Li
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
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39
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Tehrani KHME, Brüchle NC, Wade N, Mashayekhi V, Pesce D, van Haren MJ, Martin NI. Small Molecule Carboxylates Inhibit Metallo-β-lactamases and Resensitize Carbapenem-Resistant Bacteria to Meropenem. ACS Infect Dis 2020; 6:1366-1371. [PMID: 32227874 PMCID: PMC7296533 DOI: 10.1021/acsinfecdis.9b00459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the search for new inhibitors of bacterial metallo-β-lactamases (MBLs), a series of commonly used small molecule carboxylic acid derivatives were evaluated for their ability to inhibit New Delhi metallo-β-lactamase (NDM)-, Verona integron-encoded metallo-β-lactamase (VIM)-, and imipenemase (IMP)-type enzymes. Nitrilotriacetic acid (3) and N-(phosphonomethyl)iminodiacetic acid (5) showed promising activity especially against NDM-1 and VIM-2 with IC50 values in the low-to-sub μM range. Binding assays using isothermal titration calorimetry reveal that 3 and 5 bind zinc with high affinity with dissociation constant (Kd) values of 121 and 56 nM, respectively. The in vitro biological activity of 3 and 5 against E. coli expressing NDM-1 was evaluated in checkerboard format, demonstrating a strong synergistic relationship for both compounds when combined with Meropenem. Compounds 3 and 5 were then tested against 35 pathogenic strains expressing MBLs of the NDM, VIM, or IMP classes. Notably, when combined with Meropenem, compounds 3 and 5 were found to lower the minimum inhibitory concentration (MIC) of Meropenem up to 128-fold against strains producing NDM- and VIM-type enzymes.
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Affiliation(s)
- Kamaleddin H. M. E. Tehrani
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Nora C. Brüchle
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Nicola Wade
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Vida Mashayekhi
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Diego Pesce
- Laboratory of Genetics, Wageningen University and Research, 6700 AA Wageningen, The Netherlands
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthijs J. van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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40
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Lang PA, Parkova A, Leissing TM, Calvopiña K, Cain R, Krajnc A, Panduwawala TD, Philippe J, Fishwick CWG, Trapencieris P, Page MGP, Schofield CJ, Brem J. Bicyclic Boronates as Potent Inhibitors of AmpC, the Class C β-Lactamase from Escherichia coli. Biomolecules 2020; 10:E899. [PMID: 32545682 PMCID: PMC7356297 DOI: 10.3390/biom10060899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Resistance to β-lactam antibacterials, importantly via production of β-lactamases, threatens their widespread use. Bicyclic boronates show promise as clinically useful, dual-action inhibitors of both serine- (SBL) and metallo- (MBL) β-lactamases. In combination with cefepime, the bicyclic boronate taniborbactam is in phase 3 clinical trials for treatment of complicated urinary tract infections. We report kinetic and crystallographic studies on the inhibition of AmpC, the class C β‑lactamase from Escherichia coli, by bicyclic boronates, including taniborbactam, with different C-3 side chains. The combined studies reveal that an acylamino side chain is not essential for potent AmpC inhibition by active site binding bicyclic boronates. The tricyclic form of taniborbactam was observed bound to the surface of crystalline AmpC, but not at the active site, where the bicyclic form was observed. Structural comparisons reveal insights into why active site binding of a tricyclic form has been observed with the NDM-1 MBL, but not with other studied β-lactamases. Together with reported studies on the structural basis of inhibition of class A, B and D β‑lactamases, our data support the proposal that bicyclic boronates are broad-spectrum β‑lactamase inhibitors that work by mimicking a high energy 'tetrahedral' intermediate. These results suggest further SAR guided development could improve the breadth of clinically useful β-lactamase inhibition.
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Affiliation(s)
- Pauline A. Lang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; (P.A.L.); (T.M.L.); (K.C.); (A.K.); (T.D.P.)
| | - Anete Parkova
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.P.); (P.T.)
| | - Thomas M. Leissing
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; (P.A.L.); (T.M.L.); (K.C.); (A.K.); (T.D.P.)
| | - Karina Calvopiña
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; (P.A.L.); (T.M.L.); (K.C.); (A.K.); (T.D.P.)
| | - Ricky Cain
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK; (R.C.); (C.W.G.F.)
| | - Alen Krajnc
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; (P.A.L.); (T.M.L.); (K.C.); (A.K.); (T.D.P.)
| | - Tharindi D. Panduwawala
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; (P.A.L.); (T.M.L.); (K.C.); (A.K.); (T.D.P.)
| | - Jules Philippe
- Jacobs University Bremen gGmbH, 28759 Bremen, Germany; (J.P.); (M.G.P.P.)
| | | | | | - Malcolm G. P. Page
- Jacobs University Bremen gGmbH, 28759 Bremen, Germany; (J.P.); (M.G.P.P.)
| | - Christopher J. Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; (P.A.L.); (T.M.L.); (K.C.); (A.K.); (T.D.P.)
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; (P.A.L.); (T.M.L.); (K.C.); (A.K.); (T.D.P.)
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41
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Parkova A, Lucic A, Krajnc A, Brem J, Calvopiña K, Langley GW, McDonough MA, Trapencieris P, Schofield CJ. Broad Spectrum β-Lactamase Inhibition by a Thioether Substituted Bicyclic Boronate. ACS Infect Dis 2020; 6:1398-1404. [PMID: 31841636 DOI: 10.1021/acsinfecdis.9b00330] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
β-Lactamases comprise the most widely used mode of resistance to β-lactam antibiotics. Cyclic boronates have shown promise as a new class of β-lactamase inhibitor, with pioneering potential to potently inhibit both metallo- and serine-β-lactamases. We report studies concerning a bicyclic boronate ester with a thioether rather than the more typical β-lactam antibiotic "C-6/C-7" acylamino type side chain, which is present in the penicillin/cephalosporin antibiotics. The thioether bicyclic boronate ester was tested for activity against representative serine- and metallo-β-lactamases. The results support the broad inhibition potential of bicyclic boronate based inhibitors with different side chains, including against metallo-β-lactamases from B1, B2, and B3 subclasses. Combined with previous crystallographic studies, analysis of a crystal structure of the thioether inhibitor with the clinically relevant VIM-2 metallo-β-lactamase implies that further SAR work will expand the already broad scope of β-lactamase inhibition by bicyclic boronates.
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Affiliation(s)
- Anete Parkova
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Anka Lucic
- The Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Alen Krajnc
- The Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jürgen Brem
- The Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Karina Calvopiña
- The Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Gareth W. Langley
- The Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A. McDonough
- The Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | | | - Christopher J. Schofield
- The Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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42
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Lefurgy ST, Caselli E, Taracila MA, Malashkevich VN, Biju B, Papp-Wallace KM, Bonanno JB, Prati F, Almo SC, Bonomo RA. Structures of FOX-4 Cephamycinase in Complex with Transition-State Analog Inhibitors. Biomolecules 2020; 10:biom10050671. [PMID: 32349291 PMCID: PMC7277225 DOI: 10.3390/biom10050671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 12/17/2022] Open
Abstract
Boronic acid transition-state analog inhibitors (BATSIs) are partners with β-lactam antibiotics for the treatment of complex bacterial infections. Herein, microbiological, biochemical, and structural findings on four BATSIs with the FOX-4 cephamycinase, a class C β-lactamase that rapidly hydrolyzes cefoxitin, are revealed. FOX-4 is an extended-spectrum class C cephalosporinase that demonstrates conformational flexibility when complexed with certain ligands. Like other β-lactamases of this class, studies on FOX-4 reveal important insights into structure–activity relationships. We show that SM23, a BATSI, shows both remarkable flexibility and affinity, binding similarly to other β-lactamases, yet retaining an IC50 value < 0.1 μM. Our analyses open up new opportunities for the design of novel transition-state analogs of class C enzymes.
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Affiliation(s)
- Scott T. Lefurgy
- Department of Chemistry, Hofstra University, Hempstead, NY 11549, USA
| | - Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Magdalena A. Taracila
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | | | - Beena Biju
- Department of Chemistry, Hofstra University, Hempstead, NY 11549, USA
| | - Krisztina M. Papp-Wallace
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jeffrey B. Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert A. Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH 44106, USA
- Correspondence: ; Tel.: +216-791-3800 (ext. 64801); Fax: +216-231-3482
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Tooke CL, Hinchliffe P, Krajnc A, Mulholland AJ, Brem J, Schofield CJ, Spencer J. Cyclic boronates as versatile scaffolds for KPC-2 β-lactamase inhibition. RSC Med Chem 2020; 11:491-496. [PMID: 33479650 PMCID: PMC7536818 DOI: 10.1039/c9md00557a] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase-2 (KPC-2) is a serine-β-lactamase (SBL) capable of hydrolysing almost all β-lactam antibiotics. We compare KPC-2 inhibition by vaborbactam, a clinically-approved monocyclic boronate, and VNRX-5133 (taniborbactam), a bicyclic boronate in late-stage clinical development. Vaborbactam inhibition is slowly reversible, whereas taniborbactam has an off-rate indicating essentially irreversible complex formation and a 15-fold higher on-rate, although both potentiate β-lactam activity against KPC-2-expressing K. pneumoniae. High resolution X-ray crystal structures reveal closely related binding modes for both inhibitors to KPC-2, with differences apparent only in positioning of the endocyclic boronate ester oxygen. The results indicate the bicyclic boronate scaffold as both an efficient, long-lasting, KPC-2 inhibitor and capable of supporting further iterations that may improve potency against specific enzyme targets and pre-empt the emergence of inhibitor resistant KPC-2 variants.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK .
- Centre for Computational Chemistry , School of Chemistry , University of Bristol , Bristol , BS8 1TS , UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK .
| | - Alen Krajnc
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry , School of Chemistry , University of Bristol , Bristol , BS8 1TS , UK
| | - Jürgen Brem
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK
| | - Christopher J Schofield
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK
| | - James Spencer
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK .
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Linciano P, Gianquinto E, Montanari M, Maso L, Bellio P, Cebrián-Sastre E, Celenza G, Blázquez J, Cendron L, Spyrakis F, Tondi D. 4-Amino-1,2,4-triazole-3-thione as a Promising Scaffold for the Inhibition of Serine and Metallo- β-Lactamases. Pharmaceuticals (Basel) 2020; 13:E52. [PMID: 32213902 PMCID: PMC7151704 DOI: 10.3390/ph13030052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/05/2020] [Accepted: 03/21/2020] [Indexed: 02/04/2023] Open
Abstract
The emergence of bacteria that co-express serine- and metallo- carbapenemases is a threat to the efficacy of the available β-lactam antibiotic armamentarium. The 4-amino-1,2,4-triazole-3-thione scaffold has been selected as the starting chemical moiety in the design of a small library of β-Lactamase inhibitors (BLIs) with extended activity profiles. The synthesised compounds have been validated in vitro against class A serine β-Lactamase (SBLs) KPC-2 and class B1 metallo β-Lactamases (MBLs) VIM-1 and IMP-1. Of the synthesised derivatives, four compounds showed cross-class micromolar inhibition potency and therefore underwent in silico analyses to elucidate their binding mode within the catalytic pockets of serine- and metallo-BLs. Moreover, several members of the synthesised library have been evaluated, in combination with meropenem (MEM), against clinical strains that overexpress BLs for their ability to synergise carbapenems.
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Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy; (P.L.); (M.M.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10125 Turin, Italy;
| | - Martina Montanari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy; (P.L.); (M.M.)
| | - Lorenzo Maso
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (L.M.); (L.C.)
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, via Vetoio 1, 67100 L’Aquila, Italy; (P.B.); (G.C.)
| | | | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, via Vetoio 1, 67100 L’Aquila, Italy; (P.B.); (G.C.)
| | - Jesús Blázquez
- National Center of Biotechnology-CSIC, Calle Darwin 3, 28049 Madrid, Spain; (E.C.-S.); (J.B.)
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (L.M.); (L.C.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10125 Turin, Italy;
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy; (P.L.); (M.M.)
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Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-β-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance. mBio 2020; 11:mBio.03144-19. [PMID: 32184250 PMCID: PMC7078479 DOI: 10.1128/mbio.03144-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Carbapenem antibiotics are the last resort for control of severe infectious diseases, bloodstream infections, and pneumonia caused by Gram-negative bacteria, including Enterobacteriaceae. However, carbapenem-resistant Enterobacteriaceae (CRE) strains have spread globally and are a critical concern in clinical settings because CRE infections are recognized as a leading cause of increased mortality among hospitalized patients. Most CRE produce certain kinds of serine carbapenemases (e.g., KPC- and GES-type β-lactamases) or metallo-β-lactamases (MBLs), which can hydrolyze carbapenems. Although effective MBL inhibitors are expected to restore carbapenem efficacy against MBL-producing CRE, no MBL inhibitor is currently clinically available. Here, we synthesized 2,5-diethyl-1-methyl-4-sulfamoylpyrrole-3-carboxylic acid (SPC), which is a potent inhibitor of MBLs. SPC is a remarkable lead compound for clinically useful MBL inhibitors and can potentially provide a considerable benefit to patients receiving treatment for lethal infectious diseases caused by MBL-producing CRE. Production of metallo-β-lactamases (MBLs), which hydrolyze carbapenems, is a cause of carbapenem resistance in Enterobacteriaceae. Development of effective inhibitors for MBLs is one approach to restore carbapenem efficacy in carbapenem-resistant Enterobacteriaceae (CRE). We report here that sulfamoyl heteroarylcarboxylic acids (SHCs) can competitively inhibit the globally spreading and clinically relevant MBLs (i.e., IMP-, NDM-, and VIM-type MBLs) at nanomolar to micromolar orders of magnitude. Addition of SHCs restored meropenem efficacy against 17/19 IMP-type and 7/14 NDM-type MBL-producing Enterobacteriaceae to satisfactory clinical levels. SHCs were also effective against IMP-type MBL-producing Acinetobacter spp. and engineered Escherichia coli strains overproducing individual minor MBLs (i.e., TMB-2, SPM-1, DIM-1, SIM-1, and KHM-1). However, SHCs were less effective against MBL-producing Pseudomonas aeruginosa. Combination therapy with meropenem and SHCs successfully cured mice infected with IMP-1-producing E. coli and dually NDM-1/VIM-1-producing Klebsiella pneumoniae clinical isolates. X-ray crystallographic analyses revealed the inhibition mode of SHCs against MBLs; the sulfamoyl group of SHCs coordinated to two zinc ions, and the carboxylate group coordinated to one zinc ion and bound to positively charged amino acids Lys224/Arg228 conserved in MBLs. Preclinical testing revealed that the SHCs showed low toxicity in cell lines and mice and high stability in human liver microsomes. Our results indicate that SHCs are promising lead compounds for inhibitors of MBLs to combat MBL-producing CRE.
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Hecker SJ, Reddy KR, Lomovskaya O, Griffith DC, Rubio-Aparicio D, Nelson K, Tsivkovski R, Sun D, Sabet M, Tarazi Z, Parkinson J, Totrov M, Boyer SH, Glinka TW, Pemberton OA, Chen Y, Dudley MN. Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-β-lactamases. J Med Chem 2020; 63:7491-7507. [DOI: 10.1021/acs.jmedchem.9b01976] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Scott J. Hecker
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - K. Raja Reddy
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Olga Lomovskaya
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - David C. Griffith
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Debora Rubio-Aparicio
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Kirk Nelson
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Ruslan Tsivkovski
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Dongxu Sun
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Mojgan Sabet
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Ziad Tarazi
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Jonathan Parkinson
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Maxim Totrov
- Molsoft LLC, 11199 Sorrento Valley Road, San Diego, California 92121, United States
| | - Serge H. Boyer
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Tomasz W. Glinka
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Orville A. Pemberton
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Michael N. Dudley
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
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Yan Y, Li G, Li G. Principles and current strategies targeting metallo‐β‐lactamase mediated antibacterial resistance. Med Res Rev 2020; 40:1558-1592. [PMID: 32100311 DOI: 10.1002/med.21665] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 02/11/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Yu‐Hang Yan
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Gen Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Guo‐Bo Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
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VNRX-5133 (Taniborbactam), a Broad-Spectrum Inhibitor of Serine- and Metallo-β-Lactamases, Restores Activity of Cefepime in Enterobacterales and Pseudomonas aeruginosa. Antimicrob Agents Chemother 2020; 64:AAC.01963-19. [PMID: 31871094 PMCID: PMC7038240 DOI: 10.1128/aac.01963-19] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/11/2019] [Indexed: 12/24/2022] Open
Abstract
As shifts in the epidemiology of β-lactamase-mediated resistance continue, carbapenem-resistant Enterobacterales (CRE) and carbapenem-resistant Pseudomonas aeruginosa (CRPA) are the most urgent threats. Although approved β-lactam (BL)-β-lactamase inhibitor (BLI) combinations address widespread serine β-lactamases (SBLs), such as CTX-M-15, none provide broad coverage against either clinically important serine-β-lactamases (KPC, OXA-48) or clinically important metallo-β-lactamases (MBLs; e.g., NDM-1). VNRX-5133 (taniborbactam) is a new cyclic boronate BLI that is in clinical development combined with cefepime for the treatment of infections caused by β-lactamase-producing CRE and CRPA. Taniborbactam is the first BLI with direct inhibitory activity against Ambler class A, B, C, and D enzymes. From biochemical and structural analyses, taniborbactam exploits substrate mimicry while employing distinct mechanisms to inhibit both SBLs and MBLs. It is a reversible covalent inhibitor of SBLs with slow dissociation and a prolonged active-site residence time (half-life, 30 to 105 min), while in MBLs, it behaves as a competitive inhibitor, with inhibitor constant (Ki ) values ranging from 0.019 to 0.081 μM. Inhibition is achieved by mimicking the transition state structure and exploiting interactions with highly conserved active-site residues. In microbiological testing, taniborbactam restored cefepime activity in 33/34 engineered Escherichia coli strains overproducing individual enzymes covering Ambler classes A, B, C, and D, providing up to a 1,024-fold shift in the MIC. Addition of taniborbactam restored the antibacterial activity of cefepime against all 102 Enterobacterales clinical isolates tested and 38/41 P. aeruginosa clinical isolates tested with MIC90s of 1 and 4 μg/ml, respectively, representing ≥256- and ≥32-fold improvements, respectively, in antibacterial activity over that of cefepime alone. The data demonstrate the potent, broad-spectrum rescue of cefepime activity by taniborbactam against clinical isolates of CRE and CRPA.
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Tselepis L, Langley GW, Aboklaish AF, Widlake E, Jackson DE, Walsh TR, Schofield CJ, Brem J, Tyrrell JM. In vitro efficacy of imipenem-relebactam and cefepime-AAI101 against a global collection of ESBL-positive and carbapenemase-producing Enterobacteriaceae. Int J Antimicrob Agents 2020; 56:105925. [PMID: 32084512 DOI: 10.1016/j.ijantimicag.2020.105925] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 01/03/2020] [Accepted: 02/11/2020] [Indexed: 01/04/2023]
Abstract
OBJECTIVES To evaluate the potential clinical in vitro efficacy of novel β-lactam/β-lactamase-inhibitor combinations - including imipenem-relebactam (IPM-REL) and cefepime-AAI101 (enmetazobactam) (FEP-AAI) - against contemporary multidrug-resistant (MDR) Enterobacteriaceae. METHODS Agar-based MIC screening against MDR Enterobacteriaceae (n = 264) was used to evaluate the in vitro efficacy of IPM-REL and FEP-AAI, to compare the results with established combinations, and to investigate alternative β-lactam partners for relebactam (REL) and enmetazobactam (AAI). The inhibition activities of REL, AAI and the comparators avibactam (AVI) and tazobactam, against isolated recombinant β-lactamases covering representatives from all four Ambler classes of β-lactamases, were tested using a fluorescence-based assay. RESULTS Using recombinant proteins, all four inhibitors were highly active against the tested class A serine β-lactamases (SBLs). REL and AVI showed moderate activity against the Class C AmpC from Pseudomonas aeruginosa and the Class D OXA-10/-48 SBLs, but outperformed tazobactam and AAI. All tested inhibitors lacked activity against Class B metallo-β-lactamases (MBLs). In the presence of REL and IPM, but not AAI, susceptibility increased against Klebsiella pnuemoniae carbapenemase (KPC)-positive and OXA-48-positive isolates. Both aztreonam-AVI and ceftolozane-tazobactam were more effective than IPM-REL. In all the tested combinations, AAI was a more effective inhibitor of class A β-lactamases (ESBLs) than the established inhibitors. CONCLUSION The results lead to the proposal of alternative combination therapies involving REL and AAI to potentiate the use of β-lactams against clinical Gram-negative isolates expressing a variety of lactamases. They highlight the potential of novel combinations for combating strains not covered by existing therapies.
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Affiliation(s)
- Lucas Tselepis
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Gareth W Langley
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom; Charles River Laboratories, Chesterford Research Park, Saffron Walden, United Kingdom
| | - Ali F Aboklaish
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Emma Widlake
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Dana E Jackson
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Chris J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom.
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom; School of Cellular & Molecular Medicine, Biomedical Sciences Building, University Walk, Bristol, United Kingdom.
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Biochemical Activity of Vaborbactam. Antimicrob Agents Chemother 2020; 64:AAC.01935-19. [PMID: 31712199 PMCID: PMC6985712 DOI: 10.1128/aac.01935-19] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/30/2019] [Indexed: 11/20/2022] Open
Abstract
The most common mechanism of resistance to β-lactams antibiotics in Gram-negative bacteria is production of β-lactamase enzymes capable of cleaving the β-lactam ring. Inhibition of β-lactamase activity with small-molecule drugs is a proven strategy to restore the potency of many β-lactam antibiotics. Vaborbactam (formerly RPX7009) is a cyclic boronic acid β-lactamase inhibitor (BLI) with a broad spectrum of activity against various serine β-lactamases, including KPC carbapenemases. The combination of vaborbactam and meropenem is approved in the United States and Europe for the treatment of various nosocomial infections. We attempted to gain more insight into the mechanism of action of vaborbactam by conducting detailed kinetic characterization of its interaction with various recombinant His-tagged β-lactamases. Vaborbactam demonstrated potent inhibition of class A and class C enzymes with Ki values ranging from 0.022 to 0.18 μM, while inhibition of class D enzymes was rather poor, and no activity against class B β-lactamases was detected. Importantly, vaborbactam inhibited KPC-2, KPC-3, BKC-1, and SME-2 carbapenemases at 1:1 stoichiometry, while these numbers were higher for other class A and C enzymes. Vaborbactam was also shown to be a potent progressive inactivator of several enzymes, including KPCs with inactivation constants k 2/K in the range of 3.4 × 103 to 2.4 × 104 M-1 s-1 Finally, experiments on the recovery of enzyme activity demonstrated the high stability of the vaborbactam-KPC complex, with 0.000040 s-1 k off values and a corresponding residence time of 7 h, whereas the release of vaborbactam bound to other serine β-lactamases was substantially faster. The biochemical characteristics of vaborbactam described in this study may facilitate further chemical optimization efforts to develop boronic BLIs with improved affinity and broader spectrum of inhibition.
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