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Shi X, Dai Y, Lan Z, Wang S, Cui L, Xiao C, Zhao K, Li X, Liu W, Zhang Q. Interplay between the β-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design. Int J Biol Macromol 2024; 262:130041. [PMID: 38336327 DOI: 10.1016/j.ijbiomac.2024.130041] [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: 10/09/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Metallo-β-lactamases (MβLs) stand as significant resistant mechanism against β-lactam antibiotics in Gram-negative bacteria. The worldwide dissemination of New Delhi metallo-β-lactamases (NDMs) intensifies antimicrobial resistance, posing severe threats to human health due to the absence of inhibitors available in clinical therapy. L3, a flexible β-hairpin loop flanking the active site in MβLs, has been proven to wield influence over the reaction process by assuming a crucial role in substrate recognition and intermediate stabilization. In principle, it potentially retards product release from the enzyme, consequently reducing the overall turnover rate although the details regarding this aspect remain inadequately elucidated. In this study, we crystallized NDM-1 in complex with three penicillin substrates, conducted molecular dynamics simulations, and measured the steady-state kinetic parameters. These analyses consistently unveiled substantial disparities in their interactions with loop L3. We further synthesized a penicillin V derivative with increased hydrophobicity in the R1 side chain and co-crystallized it with NDM-1. Remarkably, this compound exhibited much stronger dynamic interplay with L3 during molecular dynamics simulation, showed much lower Km and kcat values, and demonstrated moderate inhibitory capacity to NDM-1 catalyzed meropenem hydrolysis. The data presented here may provide a strategic approach for designing mechanism-based MβL inhibitors focusing on structural elements external to the enzyme's active center.
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Affiliation(s)
- Xiangrui Shi
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Yujie Dai
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Zhu Lan
- Institute of Immunology, Army Medical University, Chongqing 400038, China
| | - Sheng Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Avenue, Wuhan, Hubei 430074, China
| | - Liwei Cui
- Institute of Immunology, Army Medical University, Chongqing 400038, China
| | - Chengliang Xiao
- College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Avenue, Wuhan, Hubei 430074, China
| | - Kunhong Zhao
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Minister of Education, Guizhou University, Guiyang 550025, China
| | - Xiangyang Li
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Minister of Education, Guizhou University, Guiyang 550025, China.
| | - Wei Liu
- Institute of Immunology, Army Medical University, Chongqing 400038, China.
| | - Qinghua Zhang
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China.
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Denakpo E, Naas T, Iorga BI. An updated patent review of metallo-β-lactamase inhibitors (2020-2023). Expert Opin Ther Pat 2023; 33:523-538. [PMID: 37737836 DOI: 10.1080/13543776.2023.2262763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/20/2023] [Indexed: 09/23/2023]
Abstract
INTRODUCTION Metallo-β-lactamases (MBLs) are enzymes produced by bacteria that confer resistance to most β-lactam antibiotics, including carbapenems, which have the broadest spectrum of activity. This resistance mechanism poses a significant threat to public health as it drastically reduces treatment options for severe bacterial infections. Developing effective inhibitors against MBLs is crucial to restore susceptibility to β-lactam antibiotics. AREAS COVERED This review aims to provide an updated analysis of patents describing novel MBL inhibitors and their potential therapeutic applications that were filed between January 2020 and May 2023. EXPERT OPINION Significant advancements were made in the development of selective MBL inhibitors with zinc-binding and zinc-chelating mechanisms of action. Dual inhibitors, targeting simultaneously both serine-β-lactamases (SBLs) and MBLs, represent an interesting alternative approach that is increasingly pertinent for the treatment of infections involving multiple β-lactamases from different Ambler classes. Most examples of MBL-specific inhibitors were focused on the treatment of MBL-mediated infections in Enterobacterales, where IMP-1 was a more difficult target compared with VIM-1 or NDM-1, and much less on Pseudomonas aeruginosa or Acinetobacter baumannii, which are more challenging to address.
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Affiliation(s)
- Elsa Denakpo
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Thierry Naas
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene unit, Assistance Publique/Hopitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
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Tolbatov I, Marrone A. Auranofin Targeting the NDM-1 Beta-Lactamase: Computational Insights into the Electronic Configuration and Quasi-Tetrahedral Coordination of Gold Ions. Pharmaceutics 2023; 15:pharmaceutics15030985. [PMID: 36986846 PMCID: PMC10057648 DOI: 10.3390/pharmaceutics15030985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Recently, the well-characterized metallodrug auranofin has been demonstrated to restore the penicillin and cephalosporin sensitivity in resistant bacterial strains via the inhibition of the NDM-1 beta-lactamase, which is operated via the Zn/Au substitution in its bimetallic core. The resulting unusual tetrahedral coordination of the two ions was investigated via the density functional theory calculations. By assessing several charge and multiplicity schemes, coupled with on/off constraining the positions of the coordinating residues, it was demonstrated that the experimental X-ray structure of the gold-bound NDM-1 is consistent with either Au(I)-Au(I) or Au(II)-Au(II) bimetallic moieties. The presented results suggest that the most probable mechanism for the auranofin-based Zn/Au exchange in NDM-1 includes the early formation of the Au(I)-Au(I) system, superseded by oxidation yielding the Au(II)-Au(II) species bearing the highest resemblance to the X-ray structure.
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Affiliation(s)
- Iogann Tolbatov
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Paisos Catalans 16, 43007 Tarragona, Spain
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università degli Studi "G. D'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
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Zhang Q, Wang M, Hu X, Yan A, Ho PL, Li H, Sun H. Gold drugs as colistin adjuvants in the fight against MCR-1 producing bacteria. J Biol Inorg Chem 2023; 28:225-234. [PMID: 36662362 DOI: 10.1007/s00775-022-01983-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/21/2023]
Abstract
The emergence and rapid spread of the mobile colistin resistance gene mcr-1 among bacterial species and hosts significantly challenge the efficacy of "last-line" antibiotic colistin. Previously, we reported silver nitrate and auranofin serve as colistin adjuvants for combating mcr-1-positive bacteria. Herein, we uncovered more gold-based drugs and nanoparticles, and found that they exhibited varying degree of synergisms with colistin on killing mcr-1-positive bacteria. However, pre-activation of the drugs by either glutathione or N-acetyl cysteine, thus releasing and accumulating gold ions, is perquisite for their abilities to substitute zinc cofactor from MCR-1 enzyme. X-ray crystallography and biophysical studies further supported the proposed mechanism. This study not only provides basis for combining gold-based drugs and colistin for combating mcr-1-positive bacterial infections, but also undoubtedly opens a new horizon for metabolism details of gold-based drugs in overcoming antimicrobial resistance.
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Affiliation(s)
- Qi Zhang
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics On Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Minji Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Xuqiao Hu
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics On Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Pak-Leung Ho
- Carol Yu Centre for Infection, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China.,Department of Microbiology, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Hongyan Li
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics On Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Hongzhe Sun
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics On Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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Li H, Yuan S, Wei X, Sun H. Metal-based strategies for the fight against COVID-19. Chem Commun (Camb) 2022; 58:7466-7482. [PMID: 35730442 DOI: 10.1039/d2cc01772e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed over six million lives globally to date. Despite the availability of vaccines, the pandemic still cannot be fully controlled owing to rapid mutation of the virus that renders enhanced transmissibility and antibody evasion. This is thus an unmet need to develop safe and effective therapeutic options for COVID-19, in particular, remedies that can be used at home. Considering the great success of multi-targeted cocktail therapy for the treatment of viral infections, metal-based drugs might represent a unique and new source of antivirals that resemble a cocktail therapy in terms of their mode of actions. In this review, we first summarize the role that metal ions played in SARS-CoV-2 viral replication and pathogenesis, then highlight the chemistry of metal-based strategies in the fight against SARS-CoV-2 infection, including both metal displacement and chelation based approaches. Finally, we outline a perspective and direction on how to design and develop metal-based antivirals for the fight against the current or future coronavirus pandemic.
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Affiliation(s)
- Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Shuofeng Yuan
- Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xueying Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. .,Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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Bismuth complex of quinoline thiosemicarbazone restores carbapenem sensitivity in NDM-1-positive Klebsiella pneumoniae. J Inorg Biochem 2022; 234:111887. [DOI: 10.1016/j.jinorgbio.2022.111887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022]
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