1
|
Bibi Z, Asghar I, Ashraf NM, Zeb I, Rashid U, Hamid A, Ali MK, Hatamleh AA, Al-Dosary MA, Ahmad R, Ali M. Prediction of Phytochemicals for Their Potential to Inhibit New Delhi Metallo β-Lactamase (NDM-1). Pharmaceuticals (Basel) 2023; 16:1404. [PMID: 37895875 PMCID: PMC10610165 DOI: 10.3390/ph16101404] [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: 08/09/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The effectiveness of all antibiotics in the β-lactam group to cure bacterial infections has been impaired by the introduction of the New Delhi Metallo-β-lactamase (NDM-1) enzyme. Attempts have been made to discover a potent chemical as an inhibitor to this enzyme in order to restore the efficacy of antibiotics. However, it has been a challenging task to develop broad-spectrum inhibitors of metallo-β-lactamases. Lack of sequence homology across metallo-β-lactamases (MBLs), the rapidly evolving active site of the enzyme, and structural similarities between human enzymes and metallo-β-lactamases, are the primary causes for the difficulty in the development of these inhibitors. Therefore, it is imperative to concentrate on the discovery of an effective NDM-1 inhibitor. This study used various in silico approaches, including molecular docking and molecular dynamics simulations, to investigate the potential of phytochemicals to inhibit the NDM-1 enzyme. For this purpose, a library of about 59,000 phytochemicals was created from the literature and other databases, including FoodB, IMPPAT, and Phenol-Explorer. A physiochemical and pharmacokinetics analysis was performed to determine possible toxicity and mutagenicity of the ligands. Following the virtual screening, phytochemicals were assessed for their binding with NDM-1using docking scores, RMSD values, and other critical parameters. The docking score was determined by selecting the best conformation of the protein-ligand complex. Three phytochemicals, i.e., butein (polyphenol), monodemethylcurcumin (polyphenol), and rosmarinic acid (polyphenol) were identified as result of pharmacokinetics and molecular docking studies. Furthermore, molecular dynamics simulations were performed to determine structural stabilities of the protein-ligand complexes. Monodemethylcurcumin, butein, and rosmarinic acid were identified as potential inhibitors of NDM-1 based on their low RMSD, RMSF, hydrogen bond count, average Coulomb-Schrödinger interaction energy, and Lennard-Jones-Schrödinger interaction energy. The present investigation suggested that these phytochemicals might be promising candidates for future NDM-1 medication development to respond to antibiotic resistance.
Collapse
Affiliation(s)
- Zainab Bibi
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Irfa Asghar
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of Punjab, Lahore P.O. Box 54590, Pakistan;
| | - Iftikhar Zeb
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Umer Rashid
- Department of Chemistry, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan;
| | - Arslan Hamid
- LIMES Institute, University of Bonn, D-53113 Bonn, Germany;
| | - Maria Kanwal Ali
- Institute of Nuclear Medicine, Oncology and Radiotherapy (INOR), Abbottabad 22060, Pakistan;
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.)
| | - Munirah Abdullah Al-Dosary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.)
| | - Raza Ahmad
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Muhammad Ali
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| |
Collapse
|
2
|
Xu R, Chen K, Han X, Lou Y, Gu S, Gao Y, Shang S, Song Z, Song J, Li J. Design and Synthesis of Antifungal Candidates Containing Triazole Scaffold from Natural Rosin against Valsa mali for Crop Protection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37318049 DOI: 10.1021/acs.jafc.3c02002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Two series of dehydroabietyl-1,2,4-triazole-4-Schiff-based derivatives were synthesized from rosin to control plant fungal diseases. In vitro evaluation and screening of the antifungal activity were performed using Valsa mali, Colletotrichum orbiculare, Fusarium graminearum, Sclerotinia sclerotiorum, and Gaeumannomyces graminis. Compound 3f showed excellent fungicidal activity against V. mali (EC50 = 0.537 μg/mL), which was significantly more effective than the positive control fluconazole (EC50 = 4.707 μg/mL). Compound 3f also had a considerable protective effect against V. mali (61.57%-92.16%), which was slightly lower than that of fluconazole (85.17-100%) at 25-100 μg/mL. Through physiological and biochemical analyses, the preliminary mode of action of compound 3f against V. mali was explored. Ultrastructural observation of mycelia showed that compound 3f hindered the growth of the mycelium and destroyed the ultrastructure of V. mali seriously. Conductivity analysis and laser scanning confocal microscope staining showed that compound 3f changed cell-membrane permeability and caused accumulation of reactive oxygen species. The enzyme activity results showed that compound 3f significantly inhibited the activity of CYP51 (59.70%), SOD (76.9%), and CAT (67.86%). Molecular docking identified strong interaction energy between compound 3f and crystal structures of CYP51 (-11.18 kcal/mol), SOD (-9.25 kcal/mol), and CAT (-8.79 kcal/mol). These results provide guidance for the discovery of natural product-based antifungal pesticide candidates.
Collapse
Affiliation(s)
- Renle Xu
- Jiangsu Province Key Laboratory of Biomass Energy and Materials, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Kun Chen
- Jiangsu Province Key Laboratory of Biomass Energy and Materials, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xu Han
- Jiangsu Province Key Laboratory of Biomass Energy and Materials, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yuhang Lou
- Jiangsu Province Key Laboratory of Biomass Energy and Materials, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Shihao Gu
- Jiangsu Province Key Laboratory of Biomass Energy and Materials, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yanqing Gao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Shibin Shang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing, Jiangsu 210042, People's Republic of China
| | - Zhanqian Song
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing, Jiangsu 210042, People's Republic of China
| | - Jie Song
- Department of Chemistry and Biochemistry, University of Michigan-Flint, Flint, Michigan 48502, United States
| | - Jian Li
- Jiangsu Province Key Laboratory of Biomass Energy and Materials, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| |
Collapse
|
3
|
Kong L, Zhang Y, Yang L, Yan Y, Cheng M, Wang X, Zhai L, Yang K. Synthesis and Inhibitory Activity of Oxazolethioacetamides against Metallo‐β‐Lactamase. ChemistrySelect 2023. [DOI: 10.1002/slct.202204108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lingyan Kong
- The College of Life Sciences Northwest University Xi'an 710069, Shaanxi Province P. R. China
| | - Yilin Zhang
- Shaanxi Qinling Industrial Technology Research Institute of Special Biological Resources, College of Biology Pharmacy and Food Engineering Shangluo University Shangluo 726000, Shaanxi Province P. R. China
| | - Liwen Yang
- Shaanxi Qinling Industrial Technology Research Institute of Special Biological Resources, College of Biology Pharmacy and Food Engineering Shangluo University Shangluo 726000, Shaanxi Province P. R. China
| | - Yong Yan
- Shaanxi Qinling Industrial Technology Research Institute of Special Biological Resources, College of Biology Pharmacy and Food Engineering Shangluo University Shangluo 726000, Shaanxi Province P. R. China
| | - Min Cheng
- Shaanxi Qinling Industrial Technology Research Institute of Special Biological Resources, College of Biology Pharmacy and Food Engineering Shangluo University Shangluo 726000, Shaanxi Province P. R. China
| | - Xuejun Wang
- Shaanxi Qinling Industrial Technology Research Institute of Special Biological Resources, College of Biology Pharmacy and Food Engineering Shangluo University Shangluo 726000, Shaanxi Province P. R. China
| | - Le Zhai
- Engineering Research Center of Advanced Ferroelectric Functional Materials, Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering Baoji University of Arts and Sciences Baoji 721013, Shaanxi Province P. R. China
| | - Kewu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science Northwest University Xi'an 710127, Shaanxi Province P. R. China
| |
Collapse
|
4
|
Yu T, Ahmad Malik A, Anuwongcharoen N, Eiamphungporn W, Nantasenamat C, Piacham T. Towards combating antibiotic resistance by exploring the quantitative structure-activity relationship of NDM-1 inhibitors. EXCLI JOURNAL 2022; 21:1331-1351. [PMID: 36540675 PMCID: PMC9755517 DOI: 10.17179/excli2022-5380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The emergence of New Delhi metallo-beta-lactamase-1 (NDM-1) has conferred enteric bacteria resistance to almost all beta-lactam antibiotics. Its capability of horizontal transfer through plasmids, amongst humans, animal reservoirs and the environment, has added up to the totality of antimicrobial resistance control, animal husbandry and food safety. Thus far, there have been no effective drugs for neutralizing NDM-1. This study explores the structure-activity relationship of NDM-1 inhibitors. IC50 values of NDM-1 inhibitors were compiled from both the ChEMBL database and literature. After curation, a final set of 686 inhibitors were used for machine learning model building using the random forest algorithm against 12 sets of molecular fingerprints. Benchmark results indicated that the KlekotaRothCount fingerprint provided the best overall performance with an accuracy of 0.978 and 0.778 for the training and testing set, respectively. Model interpretation revealed that nitrogen-containing features (KRFPC 4080, KRFPC 3882, KRFPC 677, KRFPC 3608, KRFPC 3750, KRFPC 4287 and KRFPC 3943), sulfur-containing substructures (KRFPC 2855 and KRFPC 4843), aromatic features (KRFPC 1566, KRFPC 1564, KRFPC 1642, KRFPC 3608, KRFPC 4287 and KRFPC 3943), carbonyl features (KRFPC 1193 and KRFPC 3025), aliphatic features (KRFPC 2975, KRFPC 297, KRFPC 3224 and KRFPC 669) are features contributing to NDM-1 inhibitory activity. It is anticipated that findings from this study would help facilitate the drug discovery of NDM-1 inhibitors by providing guidelines for further lead optimization.
Collapse
Affiliation(s)
- Tianshi Yu
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Aijaz Ahmad Malik
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nuttapat Anuwongcharoen
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Warawan Eiamphungporn
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | | | - Theeraphon Piacham
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| |
Collapse
|
5
|
A Modified Vancomycin Molecule Confers Potent Inhibitory Efficacy against Resistant Bacteria Mediated by Metallo-β-Lactamases. Molecules 2022; 27:molecules27227685. [PMID: 36431786 PMCID: PMC9693118 DOI: 10.3390/molecules27227685] [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] [Received: 09/19/2022] [Revised: 10/04/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Multidrug-resistant bacterial infections mediated by metallo-β-lactamases (MβLs) have grown into an emergent health threat, and development of novel antimicrobials is an ideal strategy to combat the infections. Herein, a novel vancomycin derivative Vb was constructed by conjugation of triazolylthioacetamide and vancomycin molecules, characterized by reverse-phase high performance liquid chromatography (HPLC) and confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The biological assays revealed that Vb effectively inhibited S. aureus and methicillin-resistant S. aureus (MRSA), gradually increased the antimicrobial effect of β-lactam antibiotics (cefazolin, meropenem and penicillin G) and exhibited a dose-dependent synergistic antibacterial effect against eight resistant strains tested, which was confirmed by the time-kill curves determination. Most importantly, Vb increased the antimicrobial effect of meropenem against the clinical isolates EC08 and EC10 and E. coli producing ImiS and CcrA, resulting in a 4- and 8-fold reduction in MIC values, respectively, at a dose up to 32 μg/mL. This work offers a promising scaffold for the development of MβLs inhibitors, specifically antimicrobials for clinically drug-resistant isolates.
Collapse
|
6
|
Gavara L, Verdirosa F, Sevaille L, Legru A, Corsica G, Nauton L, Sandra Mercuri P, Sannio F, De Luca F, Hadjadj M, Cerboni G, Vo Hoang Y, Licznar-Fajardo P, Galleni M, Docquier JD, Hernandez JF. 1,2,4-Triazole-3-thione analogues with an arylakyl group at position 4 as metallo-β-lactamase inhibitors. Bioorg Med Chem 2022; 72:116964. [PMID: 36030663 DOI: 10.1016/j.bmc.2022.116964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/22/2022] [Accepted: 08/06/2022] [Indexed: 12/31/2022]
Abstract
Metallo-β-lactamases (MBLs) represent an increasingly serious threat to public health because of their increased prevalence worldwide in relevant opportunistic Gram-negative pathogens. MBLs efficiently inactivate widely used and most valuable β-lactam antibiotics, such as oxyiminocephalosporins (ceftriaxone, ceftazidime) and the last-resort carbapenems. To date, no MBL inhibitor has been approved for therapeutic applications. We are developing inhibitors characterized by a 1,2,4-triazole-3-thione scaffold as an original zinc ligand and few promising series were already reported. Here, we present the synthesis and evaluation of a new series of compounds characterized by the presence of an arylalkyl substituent at position 4 of the triazole ring. The alkyl link was mainly an ethylene, but a few compounds without alkyl or with an alkyl group of various lengths up to a butyl chain were also synthesized. Some compounds in both sub-series were micromolar to submicromolar inhibitors of tested VIM-type MBLs. A few of them were broad-spectrum inhibitors, as they showed significant inhibitory activity on NDM-1 and, to a lesser extent, IMP-1. Among these, several inhibitors were able to significantly reduce the meropenem MIC on VIM-1- and VIM-4- producing clinical isolates by up to 16-fold. In addition, ACE inhibition was absent or moderate and one promising compound did not show toxicity toward HeLa cells at concentrations up to 250 μM. This series represents a promising basis for further exploration. Finally, molecular modelling of representative compounds in complex with VIM-2 was performed to study their binding mode.
Collapse
Affiliation(s)
- Laurent Gavara
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, Montpellier, France.
| | - Federica Verdirosa
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy
| | - Laurent Sevaille
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Alice Legru
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Giuseppina Corsica
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy
| | - Lionel Nauton
- Institut de Chimie de Clermont-Ferrand, Université Clermont-Auvergne, CNRS, Clermont-Ferrand, France
| | - Paola Sandra Mercuri
- Laboratoire des Macromolécules Biologiques, Centre d'Ingénierie des Protéines-InBioS, Université de Liège, Institute of Chemistry B6a, Sart-Tilman, 4000 Liège, Belgium
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy
| | - Filomena De Luca
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy
| | - Margot Hadjadj
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Giulia Cerboni
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy
| | - Yen Vo Hoang
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Moreno Galleni
- Laboratoire des Macromolécules Biologiques, Centre d'Ingénierie des Protéines-InBioS, Université de Liège, Institute of Chemistry B6a, Sart-Tilman, 4000 Liège, Belgium
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; Laboratoire de Bactériologie Moléculaire, Centre d'Ingénierie des Protéines-InBioS, Université de Liège, B-4000 Liège, Belgium.
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, Montpellier, France.
| |
Collapse
|
7
|
Identification of a Potential Inhibitor (MCULE-8777613195-0-12) of New Delhi Metallo-β-Lactamase-1 (NDM-1) Using In Silico and In Vitro Approaches. Molecules 2022; 27:molecules27185930. [PMID: 36144666 PMCID: PMC9504514 DOI: 10.3390/molecules27185930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in bacteria mediated by NDM-1 is an emerging threat to the public health, with an enormous economic burden. There is a scarcity in the availability of specific NDM-1 inhibitors, and also a lag in the development of new inhibitors in pharmaceutical industries. In order to identify novel inhibitors of NDM-1, we screened a library of more than 20 million compounds, available at the MCULE purchasable database. Virtual screening led to the identification of six potential inhibitors, namely, MCULE-1996250788-0-2, MCULE-8777613195-0-12, MCULE-2896881895-0-14, MCULE-5843881524-0-3, MCULE-4937132985-0-1, and MCULE-7157846117-0-1. Furthermore, analyses by molecular docking and ADME properties showed that MCULE-8777613195-0-12 was the most suitable inhibitor against NDM-1. An analysis of the binding pose revealed that MCULE-8777613195-0-12 formed four hydrogen bonds with the catalytic residues of NDM-1 (His120, His122, His189, and Cys208) and interacted with other key residues. Molecular dynamics simulation and principal component analysis confirmed the stability of the NDM-1 and MCULE-8777613195-0-12 complex. The in vitro enzyme kinetics showed that the catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics decreased significantly in the presence of MCULE-8777613195-0-12, due to poor catalytic proficiency (kcat) and affinity (Km). The IC50 value of MCULE-8777613195-0-12 (54.2 µM) was comparable to that of a known inhibitor, i.e., D-captopril (10.3 µM). In sum, MCULE-8777613195-0-12 may serve as a scaffold to further design/develop more potent inhibitors of NDM-1 and other β-lactamases.
Collapse
|
8
|
Li R, Chen X, Zhou C, Dai QQ, Yang L. Recent advances in β-lactamase inhibitor chemotypes and inhibition modes. Eur J Med Chem 2022; 242:114677. [PMID: 35988449 DOI: 10.1016/j.ejmech.2022.114677] [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: 06/17/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 11/26/2022]
Abstract
The effectiveness of β-lactam antibiotics is increasingly influenced by serine β-lactamases (SBLs) and metallo-β-lactamases (MBLs), which can hydrolyze β-lactam antibiotics. The development of effective β-lactamase inhibitors is an important direction to extend use of β-lactam antibiotics. Although six SBL inhibitors have been approved for clinical use, but no MBL inhibitors or MBL/SBL dual-action inhibitors are available so far. Broad-spectrum targeting clinically relevant MBLs and SBLs is currently desirable, while it is not easy to achieve such a purpose owing to structural and mechanistic differences between MBLs and SBLs. In this review, we summarized recent advances of inhibitor chemotypes targeting MBLs and SBLs and their inhibition mechanisms, particularly including lead discovery and structural optimization strategies, with the aim to provide useful information for future efforts to develop new MBL and SBL inhibitors.
Collapse
Affiliation(s)
- Rong Li
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, PR China
| | - Xi Chen
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, PR China
| | - Cong Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China
| | - Qing-Qing Dai
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China
| | - Lingling Yang
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, PR China.
| |
Collapse
|
9
|
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]
|
10
|
Risedronate and Methotrexate Are High-Affinity Inhibitors of New Delhi Metallo-β-Lactamase-1 (NDM-1): A Drug Repurposing Approach. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041283. [PMID: 35209073 PMCID: PMC8878330 DOI: 10.3390/molecules27041283] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/01/2023]
Abstract
Bacteria expressing New Delhi metallo-β-lactamase-1 (NDM-1) can hydrolyze β-lactam antibiotics (penicillins, cephalosporins, and carbapenems) and, thus, mediate multidrug resistance. The worldwide dissemination of NDM-1 poses a serious threat to public health, imposing a huge economic burden in the development of new antibiotics. Thus, there is an urgent need for the identification of novel NDM-1 inhibitors from a pool of already-known drug molecules. Here, we screened a library of FDA-approved drugs to identify novel non-β-lactam ring-containing inhibitors of NDM-1 by applying computational as well as in vitro experimental approaches. Different steps of high-throughput virtual screening, molecular docking, molecular dynamics simulation, and enzyme kinetics were performed to identify risedronate and methotrexate as the inhibitors with the most potential. The molecular mechanics/generalized Born surface area (MM/GBSA) and molecular dynamics (MD) simulations showed that both of the compounds (risedronate and methotrexate) formed a stable complex with NDM-1. Furthermore, analyses of the binding pose revealed that risedronate formed two hydrogen bonds and three electrostatic interactions with the catalytic residues of NDM-1. Similarly, methotrexate formed four hydrogen bonds and one electrostatic interaction with NDM-1’s active site residues. The docking scores of risedronate and methotrexate for NDM-1 were –10.543 kcal mol−1 and −10.189 kcal mol−1, respectively. Steady-state enzyme kinetics in the presence of risedronate and methotrexate showed a decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics, owing to poor catalytic proficiency and affinity. The results were further validated by determining the MICs of imipenem and meropenem in the presence of risedronate and methotrexate. The IC50 values of the identified inhibitors were in the micromolar range. The findings of this study should be helpful in further characterizing the potential of risedronate and methotrexate to treat bacterial infections.
Collapse
|
11
|
Ding M, Wan S, Wu N, Yan Y, Li J, Bao X. Synthesis, Structural Characterization, and Antibacterial and Antifungal Activities of Novel 1,2,4-Triazole Thioether and Thiazolo[3,2- b]-1,2,4-triazole Derivatives Bearing the 6-Fluoroquinazolinyl Moiety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15084-15096. [PMID: 34881871 DOI: 10.1021/acs.jafc.1c02144] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A total of 52 novel 1,2,4-triazole thioether and thiazolo[3,2-b]-1,2,4-triazole derivatives bearing the 6-fluoroquinazolinyl moiety were designed, synthesized, and evaluated as antimicrobial agents in agriculture based on the molecular hybridization strategy. Among them, molecular structures of compounds 5g and 6m were further confirmed via the single-crystal X-ray diffraction method. The bioassay results indicated that some of the target compounds possessed excellent antibacterial activities in vitro against the pathogen Xanthomonas oryzae pv. oryzae (Xoo). For example, compound 6u demonstrated a strong anti-Xoo efficacy with an EC50 value of 18.8 μg/mL, nearly 5-fold more active than that of the commercialized bismerthiazol (EC50 = 93.6 μg/mL). Moreover, the anti-Xoo mechanistic studies revealed that compound 6u exerted its antibacterial effects by increasing the permeability of bacterial membrane, reducing the content of extracellular polysaccharide, and inducing morphological changes of bacterial cells. Importantly, in vivo assays revealed its pronounced protection and curative effects against rice bacterial blight, proving its potential as a promising bactericide candidate for controlling Xoo. Moreover, compound 6u had a good pesticide-likeness based on Tice's criteria. More interestingly, compound 6u with high anti-Xoo activity also demonstrated a potent inhibitory effect of 80.8% against the fungus Rhizoctonia solani at 50 μg/mL, comparable to that of the commercialized chlorothalonil (85.9%). Overall, the current study will provide useful guidance for the rational design of more efficient agricultural antimicrobial agents using the thiazolo[3,2-b]-1,2,4-triazole derivatives bearing the 6-fluoroquinazolinyl moiety as lead compounds.
Collapse
Affiliation(s)
- Muhan Ding
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Suran Wan
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Nan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Ya Yan
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Junhong Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Xiaoping Bao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| |
Collapse
|
12
|
Chigan JZ, Li JQ, Ding HH, Xu YS, Liu L, Chen C, Yang KW. Hydroxamates as a potent skeleton for the development of metallo-β-lactamase inhibitors. Chem Biol Drug Des 2021; 99:362-372. [PMID: 34862744 DOI: 10.1111/cbdd.13990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/02/2021] [Accepted: 11/27/2021] [Indexed: 12/29/2022]
Abstract
Bacterial resistance caused by metallo-β-lactamases (MβLs) has become an emerging public health threat, and the development of MβLs inhibitor is an effective way to overcome the resistance. In this study, thirteen novel O-aryloxycarbonyl hydroxamates were constructed and assayed against MβLs. The obtained molecules specifically inhibited imipenemase-1 (IMP-1) and New Delhi metallo-β-lactamase-1, exhibiting an IC50 value in the range of 0.10-18.42 and 0.23-22.33 μM, respectively. The hydroxamate 5 was found to be the most potent inhibitor, with an IC50 of 0.1 and 0.23 μM using meropenem and cefazolin as substrates. ICP-MS analysis showed that 5 did not coordinate to the Zn(II) ions at the active site of IMP-1, while the rapid dilution, thermal shift and MALDI-TOF assays revealed that the hydroxamate formed a covalent bond with the enzyme. Cytotoxicity assays indicated that the hydroxamates have low toxicity in MCF-7 cells. This work provided a potent scaffold for the development of MβLs inhibitors.
Collapse
Affiliation(s)
- Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Yin-Sui Xu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Lu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| |
Collapse
|
13
|
Nagulapalli Venkata KC, Ellebrecht M, Tripathi SK. Efforts towards the inhibitor design for New Delhi metallo-beta-lactamase (NDM-1). Eur J Med Chem 2021; 225:113747. [PMID: 34391033 DOI: 10.1016/j.ejmech.2021.113747] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/16/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
Antimicrobial stewardship is imperative when treating bacterial infections because the misuse and overuse of antibiotics have caused pathogens to develop life-threatening resistance mechanisms. The New Delhi metallo-beta-lactamase (NDM-1) is one of many enzymes that enable bacterial resistance. NDM-1 is a more recently discovered beta-lactamase with the ability to inactivate a wide range of beta-lactam antibiotics. Multiple NDM-1 inhibitors have been designed and tested; however, due to the complexity of the NDM-1 active site, there is currently no inhibitor on the market. Consequently, an infection caused by bacteria possessing the gene for the NDM-1 enzyme is a serious and potentially fatal complication. An abundance of research has been invested over the past decade in search of an NDM-1 inhibitor. This review aims to summarize various NDM-1 inhibitor designs that have been developed in recent years.
Collapse
Affiliation(s)
| | - Morgan Ellebrecht
- St. Louis College of Pharmacy, University of Health Sciences and Pharmacy, St. Louis, MO, 63110, USA
| | - Siddharth K Tripathi
- National Center for Natural Products Research, School of Pharmacy, The University of Mississippi, University, MS, 38677, USA
| |
Collapse
|
14
|
Sun LY, Chen C, Su J, Li JQ, Jiang Z, Gao H, Chigan JZ, Ding HH, Zhai L, Yang KW. Ebsulfur and Ebselen as highly potent scaffolds for the development of potential SARS-CoV-2 antivirals. Bioorg Chem 2021; 112:104889. [PMID: 33915460 PMCID: PMC8026246 DOI: 10.1016/j.bioorg.2021.104889] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/25/2023]
Abstract
The emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised a global catastrophe. To date, there is no specific antiviral drug available to combat this virus, except the vaccine. In this study, the main protease (Mpro) required for SARS-CoV-2 viral replication was expressed and purified. Thirty-six compounds were tested as inhibitors of SARS-CoV-2 Mpro by fluorescence resonance energy transfer (FRET) technique. The half-maximal inhibitory concentration (IC50) values of Ebselen and Ebsulfur analogs were obtained to be in the range of 0.074-0.91 μM. Notably, the molecules containing furane substituent displayed higher inhibition against Mpro, followed by Ebselen 1i (IC50 = 0.074 μM) and Ebsulfur 2k (IC50 = 0.11 μM). The action mechanism of 1i and 2k were characterized by enzyme kinetics, pre-incubation and jump dilution assays, as well as fluorescent labeling experiments, which suggested that both compounds covalently and irreversibly bind to Mpro, while molecular docking suggested that 2k formed an SS bond with the Cys145 at the enzymatic active site. This study provides two very potent scaffolds Ebsulfur and Ebselen for the development of covalent inhibitors of Mpro to combat COVID-19.
Collapse
Affiliation(s)
- Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jianpeng Su
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Zhihui Jiang
- Department of Pharmacy, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, PR China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Le Zhai
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 72101, Shaanxi Province, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
| |
Collapse
|
15
|
Gao H, Li JQ, Kang PW, Chigan JZ, Wang H, Liu L, Xu YS, Zhai L, Yang KW. N-acylhydrazones confer inhibitory efficacy against New Delhi metallo-β-lactamase-1. Bioorg Chem 2021; 114:105138. [PMID: 34229201 DOI: 10.1016/j.bioorg.2021.105138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 01/23/2023]
Abstract
The expression of β-lactamases, especially metallo-β-lactamases (MβLs) in bacteria is one of the main causes of drug resistance. In this work, an effective N-acylhydrazone scaffold as MβL inhibitor was constructed and characterized. The biological activity assays indicated that the synthesized N-acylhydrazones 1-11 preferentially inhibited MβL NDM-1, and 1 was found to be the most effective inhibitor with an IC50 of 1.2 µM. Analysis of IC50 data revealed a structure-activity relationship, which is that the pyridine and hydroxylbenzene substituents at 2-position improved inhibition of the compounds on NDM-1. ITC and enzyme kinetics assays suggested that it reversibly and competitively inhibited NDM-1 (Ki = 0.29 ± 0.05 µM). The synthesized N-acylhydrazones showed synergistic antibacterial activities with meropenem, reduced 4-16-fold MIC of meropenem on NDM-1- producing E. coli BL21 (DE3), while 1 restored 4-fold activity of meropenem on K. pneumonia expressing NDM-1 (NDM-K. pneumoniae). The mice experiments suggested that 1 combined meropenem to fight against NDM-K. pneumoniae infection in the spleen and liver. Cytotoxicity assays showed that 1 and 2 have low cytotoxicity. This study offered a new framework for the development of NDM-1 inhibitors.
Collapse
Affiliation(s)
- Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Peng-Wei Kang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Huan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Lu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Yin-Sui Xu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Le Zhai
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 72101, Shaanxi Province, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
| |
Collapse
|
16
|
Wang T, Xu K, Zhao L, Tong R, Xiong L, Shi J. Recent research and development of NDM-1 inhibitors. Eur J Med Chem 2021; 223:113667. [PMID: 34225181 DOI: 10.1016/j.ejmech.2021.113667] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/26/2021] [Accepted: 06/13/2021] [Indexed: 10/21/2022]
Abstract
Bacteria carrying New Delhi metallo-β-lactamase-1 (New Delhi metallo-β-lactamase, NDM-1) resistance gene is a new type of "superbug", which can hydrolyze almost all β-lactam antibiotics, rapidly spread among the same species and even spread among different species. NDM-1 belongs to the class B1 broad-spectrum enzyme of β-lactamase. The two positively charged zinc ions in the active center have electrostatic interaction with the hydroxyl ions in them to seize the hydrogen atom near the water molecule to form a bridging ring water molecule, which strengthens its nucleophilicity and attacks the carbonyl group on the lactam ring; thus, catalyzing the hydrolysis of β-lactam antibiotics. Since NDM-1 has an open active site and unique electrostatic structure, it essentially provides a wider range of substrate specificity. Due to its flexible hydrolysis mechanism and more and more variants also aggravate the threat of drug-resistant bacteria infection, there is still no effective inhibitor in clinic, which is a serious threat to human health and public health safety. The electron-rich substituents of NDM-1 inhibitors coordinate with two positively charged zinc ions in the active center of the enzyme through ion-dipole interaction to produce NDM-1 inhibitory activity. In this review, the research progress of NDM-1 enzyme and its inhibitors in the past 5 years was reviewed. The crystal structure, active center structure, surrounding important amino acid residues, newly discovered inhibitors and their action mechanism are classified and summarized in detail, which can be used as a reference for the development of effective drugs against drug-resistant bacteria targeting NDM-1.
Collapse
Affiliation(s)
- Ting Wang
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Kaiju Xu
- Department of Infectious Diseases, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, 610072, China
| | - Liyun Zhao
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Rongsheng Tong
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Liang Xiong
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Jianyou Shi
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| |
Collapse
|
17
|
Zhou W, Xu C, Dong G, Qiao H, Yang J, Liu H, Ding L, Sun K, Zhao W. Development of phenyltriazole thiol-based derivatives as highly potent inhibitors of DCN1-UBC12 interaction. Eur J Med Chem 2021; 217:113326. [PMID: 33756127 DOI: 10.1016/j.ejmech.2021.113326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/25/2021] [Accepted: 02/20/2021] [Indexed: 11/26/2022]
Abstract
Defective in cullin neddylation 1(DCN1) is a co-E3 ligase that is important for cullin neddylation. Dysregulation of DCN1 highly correlates with the development of various cancers. Herein, from the initial high-throughput screening, a novel hit compound 5a containing a phenyltriazole thiol core (IC50 value of 0.95 μM for DCN1-UBC12 interaction) was discovered. Further structure-based optimization leads to the development of SK-464 (IC50 value of 26 nM). We found that SK-464 not only directly bound to DCN1 in vitro, but also engaged cellular DCN1, suppressed the neddylation of cullin3, and hindered the migration and invasion of two DCN1-overexpressed squamous carcinoma cell lines (KYSE70 and H2170). These findings indicate that SK-464 may be a novel lead compound targeting DCN1-UBC12 interaction.
Collapse
Affiliation(s)
- Wenjuan Zhou
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China; Department of Pathology, Oslo University Hospital, Faculty of Medicine, University of Oslo, Oslo, 0379, Norway
| | - Chenhao Xu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China
| | - Guanjun Dong
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China
| | - Hui Qiao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China
| | - Jing Yang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China
| | - Hongmin Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China
| | - Lina Ding
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China.
| | - Kai Sun
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China.
| | - Wen Zhao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences and Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China.
| |
Collapse
|
18
|
Zhang YJ, Zhai L, Wan Y, Yang KW. Triazolylthioacetamides Confer Inhibitory Efficacy against Metallo-β- Lactamase IMP-1. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999200831094019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background: :
The appearance of antibiotic resistance caused by metallo-β-lactamases
(MβLs) is a global public health threat. Developing MβLs inhibitor is an effective way to overcome
antibiotic resistance. Recently, azolylthioacetamides were reported to be promising MβLs inhibitors.
Methods::
Triazolylthioacetamides were synthesized and tested for inhibition activity against the
purified MβL IMP-1. Antimicrobial activities of these inhibitors in combination with cefazolin were
evaluated. Isothermal Titration Calorimetry (ITC) was employed to characterize the binding of the
inhibitor to IMP-1, and their action mechanism was studied by molecular docking.
Results:
Twenty compounds exhibited specific inhibitory activity against IMP-1 with an IC50 value
in the range of 3.1-62.5 μM. Eight of the compounds can restore the antibacterial efficacy of
cefazolin against E. coli BL21 strain producing IMP-1 by 2-4 fold. ITC monitoring showed that 1c
exhibited dose-dependent inhibition on IMP-1. Docking studies revealed that the triazole group in
1c and 2d played an essential role in the inhibition activity. Cytotoxicity assay showed that 1c and
2d have low toxicity in L929 mouse fibroblastic cells.
Conclusion: :
The triazolylthioacetamides are efficient inhibitors of IMP-1 in vitro and in vivo.
Collapse
Affiliation(s)
| | - Le Zhai
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China
| | - Yi Wan
- Microbiology Institute of Shaanxi, Xi’an 710043, China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China
| |
Collapse
|
19
|
Novel 1,2,4-triazole derivatives as apoptotic inducers targeting p53: Synthesis and antiproliferative activity. Bioorg Chem 2020; 105:104369. [PMID: 33091670 DOI: 10.1016/j.bioorg.2020.104369] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 09/12/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
A series of novel thiazolo[3,2-b][1,2,4]-triazoles 3a-n has been synthesized and evaluated in vitro as potential antiproliferative. Compounds 3b-d exhibited significant antiproliferative activity. Compound 3b was the most potent with Mean GI50 1.37 µM comparing to doxorubicin (GI50 1.13 µM). The transcription effects of 3b, 3c and 3d on the p53 were assessed and compared with the reference doxorubicin. The results revealed an increase of 15-27 in p53 level compared to the test cells and that p53 protein level of 3b, 3c and 3d was significantly inductive (1419, 571 and 787 pg/mL, respectively) in relation to doxorubicin (1263 pg/mL). The docking study of the new compounds 3a-n revealed high binding scores for the new compounds toward p53 binding domain in MDM2. The docking analyses revealed the highest affinities for compounds 3b-d which induced p53 activity in MCF-7 cancer cells. Compound 3b which exhibited the highest antiproliferative activity and induced the highest increase in p53 level in MCF-7 cells showed also the highest affinity to MDM2.
Collapse
|
20
|
Andersson H, Jarvoll P, Yang SK, Yang KW, Erdélyi M. Binding of 2-(Triazolylthio)acetamides to Metallo-β-lactamase CcrA Determined with NMR. ACS OMEGA 2020; 5:21570-21578. [PMID: 32905426 PMCID: PMC7469393 DOI: 10.1021/acsomega.0c02187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/31/2020] [Indexed: 05/06/2023]
Abstract
Metallo-β-lactamase (MBL)-producing bacteria resistant to β-lactam antibiotics are a serious threat to human health. Despite great efforts and important progress in the discovery of MBL inhibitors (MBLIs), there is none in clinical use. Herein, inhibitor complexes of the MBL CcrA were investigated by NMR spectroscopy to provide perspectives on the further development of 2-(triazolylthio)acetamide-type MBLIs. By using the NMR-based chemical shift perturbation (CSP) and direction of CSP methodologies together with molecular docking, the spatial orientation of three compounds in the CcrA active site was investigated (4-6). Inhibitor 6 showed the best binding affinity (K d ≈ 2.3 ± 0.3 μM), followed by 4 (K d = 11 ± 11 μM) and 5 (K d = 34 ± 43 μM), as determined from the experimental NMR data. Based on the acquired knowledge, analogues of other MBLIs (1-3) were designed and evaluated in silico with the purpose of examining a strategy for promoting their interactions with the catalytic zinc ions.
Collapse
Affiliation(s)
- Hanna Andersson
- Department
of Chemistry—BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Patrik Jarvoll
- Centre
for Antibiotic Resistance Research (CARe) at the University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Shao-Kang Yang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127 Xi’an, P. R. China
| | - Ke-Wu Yang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127 Xi’an, P. R. China
| | - Máté Erdélyi
- Department
of Chemistry—BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
- Centre
for Antibiotic Resistance Research (CARe) at the University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| |
Collapse
|
21
|
New Delhi metallo-β-lactamase-1 inhibitors for combating antibiotic drug resistance: recent developments. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02580-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
22
|
Sharma S, Sharma S, Singh PP, Khan IA. Potential Inhibitors Against NDM-1 Type Metallo-β-Lactamases: An Overview. Microb Drug Resist 2020; 26:1568-1588. [PMID: 32486911 DOI: 10.1089/mdr.2019.0315] [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] [Indexed: 11/13/2022] Open
Abstract
A new member of the class metallo-β-lactamase (MBL), New Delhi metallo-beta-lactamase 1 (NDM-1) has emerged recently as a leading threat to the treatment of infections that have spread in all major Gram-negative pathogens. The enzyme inactivates antibiotics of the carbapenem family, which are a mainstay for the treatment of antibiotic-resistant bacterial infections. This review provides information about NDM-1 spatial structure, potential features of the active site, and its mechanism of action. It also enlists the inhibitors/compounds/drugs against NDM-1 in various development phases. Understanding their mode of inhibition and the structure-activity relationship would be beneficial for development, synthesis, and even increasing biological efficacy of inhibitors, making them more promising drug candidates.
Collapse
Affiliation(s)
- Smriti Sharma
- Clinical Microbiology Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu Tawi, India.,Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu Tawi, India
| | - Sumit Sharma
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu Tawi, India.,Medicinal Chemistry Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu Tawi, India
| | - Parvinder Pal Singh
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu Tawi, India.,Medicinal Chemistry Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu Tawi, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu Tawi, India.,Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu Tawi, India
| |
Collapse
|
23
|
Rivière G, Oueslati S, Gayral M, Créchet JB, Nhiri N, Jacquet E, Cintrat JC, Giraud F, van Heijenoort C, Lescop E, Pethe S, Iorga BI, Naas T, Guittet E, Morellet N. NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-β-Lactamase-1 and on the Binding with Flavonols as Inhibitors. ACS OMEGA 2020; 5:10466-10480. [PMID: 32426604 PMCID: PMC7226869 DOI: 10.1021/acsomega.0c00590] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/15/2020] [Indexed: 05/22/2023]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) has recently emerged as a global threat because of its ability to confer resistance to all common β-lactam antibiotics. Understanding the molecular basis of β-lactam hydrolysis by NDM is crucial for designing NDM inhibitors or β-lactams resistant to their hydrolysis. In this study, for the first time, NMR was used to study the influence of Zn(II) ions on the dynamic behavior of NDM-1. Our results highlighted that the binding of Zn(II) in the NDM-1 active site induced several structural and dynamic changes on active site loop 2 (ASL2) and L9 loops and on helix α2. We subsequently studied the interaction of several flavonols: morin, quercetin, and myricetin were identified as natural and specific inhibitors of NDM-1. Quercetin conjugates were also synthesized in an attempt to increase the solubility and bioavailability. Our NMR investigations on NDM-1/flavonol interactions highlighted that both Zn(II) ions and the residues of the NDM-1 ASL1, ASL2, and ASL4 loops are involved in the binding of flavonols. This is the first NMR interaction study of NDM-1/inhibitors, and the models generated using HADDOCK will be useful for the rational design of more active inhibitors, directed against NDM-1.
Collapse
Affiliation(s)
- Gwladys Rivière
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Saoussen Oueslati
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Maud Gayral
- Institut
de Chimie Moléculaire et des Matériaux d’Orsay
(ICMMO), CNRS, Université Paris Sud, Université Paris-Saclay, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | | | - Naïma Nhiri
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Eric Jacquet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Jean-Christophe Cintrat
- Service
de Chimie Bio-organique et Marquage (SCBM), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif/Yvette, France
| | - François Giraud
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Ewen Lescop
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Stéphanie Pethe
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Bogdan I. Iorga
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Thierry Naas
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- . Phone:(33)145212019 or (33)145213030. Fax: (33)145216340
| | - Eric Guittet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Nelly Morellet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
- . Phone:(33)169823762. Fax: (33)169823784
| |
Collapse
|
24
|
Chen C, Sun LY, Gao H, Kang PW, Li JQ, Zhen JB, Yang KW. Identification of Cisplatin and Palladium(II) Complexes as Potent Metallo-β-lactamase Inhibitors for Targeting Carbapenem-Resistant Enterobacteriaceae. ACS Infect Dis 2020; 6:975-985. [PMID: 32119777 DOI: 10.1021/acsinfecdis.9b00385] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The emergence and prevalence of carbapenem-resistant bacterial infection have seriously threatened the clinical use of almost all β-lactam antibacterials. The development of effective metallo-β-lactamase (MβL) inhibitors to restore the existing antibiotics efficacy is an ideal alternative. Although several types of serine-β-lactamase inhibitors have been successfully developed and used in clinical settings, MβL inhibitors are not clinically available to date. Herein, we identified that cisplatin and Pd(II) complexes are potent broad-spectrum inhibitors of the B1 and B2 subclasses of MβLs and effectively revived Meropenem efficacy against MβL-expressing bacteria in vitro. Enzyme kinetics, thermodynamics, inductively coupled plasma atomic emission spectrometry (ICP-AES), matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS), and site-directed mutation assays revealed that these metal complexes irreversibly inhibited NDM-1 through a novel inhibition mode involving binding to Cys208 and displacing one Zn(II) ion of the enzyme with one Pt(II) containing two NH3's or one Pd(II) ion. Importantly, the combination therapy of Meropenem and metal complexes significantly suppressed the development of higher-level resistance in bacteria producing NDM-1, also effectively reduced the bacterial burden in liver and spleen of mice infected by carbapenem-resistant Enterobacteriaceae producing NDM-1. These findings will offer potential lead compounds for the further development of clinically useful inhibitors targeting MβLs.
Collapse
Affiliation(s)
- Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Peng-Wei Kang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Jian-Bin Zhen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| |
Collapse
|
25
|
Guo H, Cheng K, Gao Y, Bai W, Wu C, He W, Li C, Li Z. A novel potent metal-binding NDM-1 inhibitor was identified by fragment virtual, SPR and NMR screening. Bioorg Med Chem 2020; 28:115437. [DOI: 10.1016/j.bmc.2020.115437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
|
26
|
Synthesis and Bioactivity of Thiazolethioacetamides as Potential Metallo-β-Lactamase Inhibitors. Antibiotics (Basel) 2020; 9:antibiotics9030099. [PMID: 32110966 PMCID: PMC7175138 DOI: 10.3390/antibiotics9030099] [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: 02/02/2020] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 11/16/2022] Open
Abstract
Metallo-β-lactamase (MβLs) mediated antibiotic resistance seriously threatens the treatment of bacterial diseases. Recently, we found that thioacetamides can be a potential MβL inhibitor skeleton. In order to improve the information of the skeleton, twelve new thiazolethioacetamides were designed by modifying the aromatic substituent. Biological activity assays identify the thiazolethioacetamides can inhibit ImiS with IC50 values of 0.17 to 0.70 μM. For two of them, the IC50 values against VIM-2 were 2.2 and 19.2 μM, which is lower than in our previous report. Eight of the thiazolethioacetamides are able to restore antibacterial activity of cefazolin against E.coli-ImiS by 2-4 fold. An analysis of the structure-activity relation and molecule docking show that the style and position of electron withdrawing groups in aromatic substituents play a crucial role in the inhibitory activity of thiazolethioacetamides. These results indicate that thiazolethioacetamides can serve as a potential skeleton of MβL inhibitors.
Collapse
|
27
|
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
| |
Collapse
|
28
|
Liu Y, Chen C, Sun LY, Gao H, Zhen JB, Yang KW. meta-Substituted benzenesulfonamide: a potent scaffold for the development of metallo-β-lactamase ImiS inhibitors. RSC Med Chem 2020; 11:259-267. [PMID: 33479632 PMCID: PMC7412727 DOI: 10.1039/c9md00455f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/26/2019] [Indexed: 01/25/2023] Open
Abstract
Metallo-β-lactamase (MβL) ImiS contributes to the emergence of carbapenem resistance. A potent scaffold, meta-substituted benzenesulfonamide, was constructed and assayed against MβLs. The twenty-one obtained molecules specifically inhibited ImiS (IC50 = 0.11-9.3 μM); 2g was found to be the best inhibitor (IC50 = 0.11 μM), and 1g and 2g exhibited partially mixed inhibition with K i of 8.0 and 0.55 μM. The analysis of the structure-activity relationship revealed that the meta-substitutes improved the inhibitory activity of the inhibitors. Isothermal titration calorimetry (ITC) assays showed that 2g reversibly inhibited ImiS. The benzenesulfonamides exhibited synergistic antibacterial effects against E. coli BL21 (DE3) cells with ImiS, resulting in a 2-4-fold reduction in the MIC of imipenem and meropenem. Also, mouse experiments showed that 2g had synergistic efficacy with meropenem and significantly reduced the bacterial load in the spleen and liver after a single intraperitoneal dose. Tracing the ImiS in living E. coli cells by RS at a super-resolution level (3D-SIM) showed that the target was initially associated on the surface of the cells, then there was a high density of uniform localization distributed in the cytosol of cells, and it finally accumulated in the formation of inclusion bodies at the cell poles. Docking studies suggested that the sulfonamide group acted as a zinc-binding group to coordinate with Zn(ii) and the residual amino acid within the CphA active center, tightly anchoring the inhibitor at the active site. This study provides a highly promising scaffold for the development of inhibitors of ImiS, even the B2 subclasses of MβLs.
Collapse
Affiliation(s)
- Ya Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Jian-Bin Zhen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| |
Collapse
|
29
|
Xiang Y, Zhang YJ, Ge Y, Zhou Y, Chen C, Wahlgren WY, Tan X, Chen X, Yang KW. Kinetic, Thermodynamic, and Crystallographic Studies of 2-Triazolylthioacetamides as Verona Integron-Encoded Metallo-β-Lactamase 2 (VIM-2) Inhibitor. Biomolecules 2020; 10:E72. [PMID: 31906402 PMCID: PMC7022493 DOI: 10.3390/biom10010072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/19/2019] [Accepted: 12/24/2019] [Indexed: 01/23/2023] Open
Abstract
Inhibition of β-lactamases presents a promising strategy to restore the β-lactams antibacterial activity to resistant bacteria. In this work, we found that aromatic carboxyl substituted 2-triazolylthioacetamides 1a-j inhibited VIM-2, exhibiting an IC50 value in the range of 20.6-58.6 μM. The structure-activity relationship study revealed that replacing the aliphatic carboxylic acid with aromatic carboxyl improved the inhibitory activity of 2-triazolylthioacetamides against VIM-2. 1a-j (16 mg/mL) restored the antibacterial activity of cefazolin against E. coli cell expressing VIM-2, resulting in a 4-8-fold reduction in MICs. The isothermal titration calorimetry (ITC) characterization suggested that the primary binding 2-triazolylthioacetamide (1b, 1c, or 1h) to VIM-2 was a combination of entropy and enthalpy contributions. Further, the crystal structure of VIM-2 in complex with 1b was obtained by co-crystallization with a hanging-drop vapour-diffusion method. The crystal structure analysis revealed that 1b bound to two Zn(II) ions of the enzyme active sites, formed H-bound with Asn233 and structure water molecule, and interacted with the hydrophobic pocket of enzyme activity center utilizing hydrophobic moieties; especially for the phenyl of aromatic carboxyl which formed π-π stacking with active residue His263. These studies confirmed that aromatic carboxyl substituted 2-triazolylthioacetamides are the potent VIM-2 inhibitors scaffold and provided help to further optimize 2-triazolylthioacetamides as VIM-2 even or broad-spectrum MβLs inhibitors.
Collapse
Affiliation(s)
- Yang Xiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (Y.X.)
- School of Physical Education, Yan’an University, Yan’an 716000, China
| | - Yue-Juan Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (Y.X.)
| | - Ying Ge
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (Y.X.)
| | - Yajun Zhou
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (Y.X.)
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Gothenburg, Sweden
| | - Xiangshi Tan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (Y.X.)
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (Y.X.)
| |
Collapse
|
30
|
Ge Y, Xu LW, Liu Y, Sun LY, Gao H, Li JQ, Yang K. Dithiocarbamate as a Valuable Scaffold for the Inhibition of Metallo-β-Lactmases. Biomolecules 2019; 9:biom9110699. [PMID: 31694268 PMCID: PMC6920875 DOI: 10.3390/biom9110699] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 01/02/2023] Open
Abstract
The 'superbug' infection caused by metallo-β-lactamases (MβLs) has grown into an emergent health threat. Given the clinical importance of MβLs, a novel scaffold, dithiocarbamate, was constructed. The obtained molecules, DC1, DC8 and DC10, inhibited MβLs NDM-1, VIM-2, IMP-1, ImiS and L1 from all three subclasses, exhibiting an IC50 < 26 μM. DC1 was found to be the best inhibitor of ImiS (IC50 < 0.22 μM). DC1-2, DC4, DC8 and DC10 restored antimicrobial effects of cefazolin and imipenem against E. coli-BL21, producing NDM-1, ImiS or L1, and DC1 showed the best inhibition of E. coli cells, expressing the three MβLs, resulting in a 2-16-fold reduction in the minimum inhibitory concentrations (MICs) of both antibiotics. Kinetics and isothermal titration calorimetry (ITC) assays showed that DC1 exhibited a reversible, and partially mixed inhibition, of NDM-1, ImiS and L1, with Ki values of 0.29, 0.14 and 5.06 µM, respectively. Docking studies suggest that the hydroxyl and carbonyl groups of DC1 form coordinate bonds with the Zn (II) ions, in the active center of NDM-1, ImiS and L1, thereby inhibiting the activity of the enzymes. Cytotoxicity assays showed that DC1, DC3, DC7 and DC9 have low toxicity in L929 mouse fibroblastic cells, at a dose of up to 250 μM. These studies revealed that the dithiocarbamate is a valuable scaffold for the development of MβLs inhibitors.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Kewu Yang
- Correspondence: ; Tel./Fax: +86-29-8153-5035
| |
Collapse
|
31
|
Shi C, Chen J, Xiao B, Kang X, Lao X, Zheng H. Discovery of NDM-1 inhibitors from natural products. J Glob Antimicrob Resist 2019; 18:80-87. [DOI: 10.1016/j.jgar.2019.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 11/15/2022] Open
|
32
|
Meng Z, Tang ML, Yu L, Liang Y, Han J, Zhang C, Hu F, Yu JM, Sun X. Novel Mercapto Propionamide Derivatives with Potent New Delhi Metallo-β-Lactamase-1 Inhibitory Activity and Low Toxicity. ACS Infect Dis 2019; 5:903-916. [PMID: 30838850 DOI: 10.1021/acsinfecdis.8b00366] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The emergence and worldwide prevalence of New Delhi metallo-β-lactamase 1 (NDM-1) expressing Gram-negative bacteria with resistance against most β-lactam antibiotics pose a serious threat to human health. However, no NDM-1 inhibitors are clinically approved at present. Herein, based on the lead compound captopril, a series of compounds were designed, synthesized, and evaluated for NDM-1 inhibitory activities. All designed compounds showed single digit micromolar or submicromolar NDM-1 inhibitory activities, which were much more potent than that of captopril. Among them, compounds 14a and 14m exhibited excellent NDM-1 inhibitory activities, with IC50 values of 0.10 and 0.12 μM, respectively. Further studies demonstrated that compound 14m displayed low cytotoxicity, good water solubility, high metabolic stability, and low acute toxicity in mice. Importantly, compound 14m exhibited potent synergistic antimicrobial activities with Meropenem (MEM) for the treatment of clinically isolated NDM-1-expressing strains.
Collapse
Affiliation(s)
- Zhi Meng
- Department of Natural Products Chemistry, School of PharmacyFudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Mei-Lin Tang
- Department of Natural Products Chemistry, School of PharmacyFudan University, 826 Zhangheng Road, Shanghai 201203, China
- State Key Laboratory of Molecular Engineering and Institutes of Biomedical Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Liting Yu
- Department of Natural Products Chemistry, School of PharmacyFudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Yongxi Liang
- Department of Natural Products Chemistry, School of PharmacyFudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jilai Han
- Department of Natural Products Chemistry, School of PharmacyFudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - ChenChen Zhang
- Department of Natural Products Chemistry, School of PharmacyFudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Fupin Hu
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Jian-Ming Yu
- Department of Natural Products Chemistry, School of PharmacyFudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Xun Sun
- Department of Natural Products Chemistry, School of PharmacyFudan University, 826 Zhangheng Road, Shanghai 201203, China
| |
Collapse
|
33
|
Shi C, Chen J, Kang X, Shen X, Lao X, Zheng H. Approaches for the discovery of metallo‐β‐lactamase inhibitors: A review. Chem Biol Drug Des 2019; 94:1427-1440. [DOI: 10.1111/cbdd.13526] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Cheng Shi
- School of Life Science and Technology China Pharmaceutical University Nanjing China
| | - Jiaxing Chen
- School of Life Science and Technology China Pharmaceutical University Nanjing China
| | - Xinyue Kang
- School of Life Science and Technology China Pharmaceutical University Nanjing China
| | - Xutong Shen
- School of Life Science and Technology China Pharmaceutical University Nanjing China
| | - Xingzhen Lao
- School of Life Science and Technology China Pharmaceutical University Nanjing China
| | - Heng Zheng
- School of Life Science and Technology China Pharmaceutical University Nanjing China
| |
Collapse
|
34
|
Kaushik A, Kaushik M, Lather V, Dua J. Recent Review on Subclass B1 Metallo-β-lactamases Inhibitors: Sword for Antimicrobial Resistance. Curr Drug Targets 2019; 20:756-762. [DOI: 10.2174/1389450120666181217101812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/03/2018] [Accepted: 12/11/2018] [Indexed: 01/17/2023]
Abstract
An emerging crisis of antibiotic resistance for microbial pathogens is alarming all the nations,
posing a global threat to human health. The production of the metallo-β-lactamase enzyme is the
most powerful strategy of bacteria to produce resistance. An efficient way to combat this global health
threat is the development of broad/non-specific type of metallo-β-lactamase inhibitors, which can inhibit
the different isoforms of the enzyme. Till date, there are no clinically active drugs against metallo-
β-lactamase. The lack of efficient drug molecules against MBLs carrying bacteria requires continuous
research efforts to overcome the problem of multidrug-resistance bacteria. The present review will
discuss the clinically potent molecules against different variants of B1 metallo-β-lactamase.
Collapse
Affiliation(s)
| | | | - Viney Lather
- Amity institute of Pharmacy, Amity University, Noida, India
| | - J.S. Dua
- School of Pharmacy, MMU, Sadopur, Ambala, India
| |
Collapse
|
35
|
Halogen-Substituted Triazolethioacetamides as a Potent Skeleton for the Development of Metallo-β-Lactamase Inhibitors. Molecules 2019; 24:molecules24061174. [PMID: 30934584 PMCID: PMC6471427 DOI: 10.3390/molecules24061174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/13/2019] [Accepted: 03/23/2019] [Indexed: 11/17/2022] Open
Abstract
Metallo-β-lactamases (MβLs) are the target enzymes of β-lactam antibiotic resistance, and there are no effective inhibitors against MβLs available for clinic so far. In this study, thirteen halogen-substituted triazolethioacetamides were designed and synthesized as a potent skeleton of MβLs inhibitors. All the compounds displayed inhibitory activity against ImiS with an IC50 value range of 0.032⁻15.64 μM except 7. The chlorine substituted compounds (1, 2 and 3) inhibited NDM-1 with an IC50 value of less than 0.96 μM, and the fluorine substituted 12 and 13 inhibited VIM-2 with IC50 values of 38.9 and 2.8 μM, respectively. However, none of the triazolethioacetamides exhibited activity against L1 at inhibitor concentrations of up to 1 mM. Enzyme inhibition kinetics revealed that 9 and 13 are mixed inhibitors for ImiS with Ki values of 0.074 and 0.27μM using imipenem as the substrate. Docking studies showed that 1 and 9, which have the highest inhibitory activity against ImiS, fit the binding site of CphA as a replacement of ImiS via stable interactions between the triazole group bridging ASP120 and hydroxyl group bridging ASN233.
Collapse
|
36
|
Zhang YJ, Liu XL, Wang WM, Chen C, Zhao MH, Yang KW. Amino Acid Thioesters Exhibit Inhibitory Activity against B1–B3 Subclasses of Metallo-β-lactamases. Chem Pharm Bull (Tokyo) 2019; 67:135-142. [DOI: 10.1248/cpb.c18-00717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yue-Juan Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University
| | - Xiao-Long Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University
| | - Wen-Ming Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University
| | - Mu-Han Zhao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University
| |
Collapse
|
37
|
Linciano P, Cendron L, Gianquinto E, Spyrakis F, Tondi D. Ten Years with New Delhi Metallo-β-lactamase-1 (NDM-1): From Structural Insights to Inhibitor Design. ACS Infect Dis 2019; 5:9-34. [PMID: 30421910 DOI: 10.1021/acsinfecdis.8b00247] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The worldwide emergence of New Delhi metallo-β-lactamase-1 (NDM-1) as a carbapenemase able to hydrolyze nearly all available β-lactam antibiotics has characterized the past decade, endangering efficacious antibacterial treatments. No inhibitors for NDM-1 are available in therapy, nor are promising compounds in the pipeline for future NDM-1 inhibitors. We report the studies dedicated to the design and development of effective NDM-1 inhibitors. The discussion for each agent moves from the employed design strategy to the ability of the identified inhibitor to synergize β-lactam antibiotics. A structural analysis of NDM-1 mechanism of action based on selected X-ray complexes is also reported: the intrinsic flexibility of the binding site and the comparison between penicillin/cephalosporin and carbapenem mechanisms of hydrolysis are evaluated. Despite the valuable progress in terms of structural and mechanistic information, the design of a potent NDM-1 inhibitor to be introduced in therapy remains challenging. Certainly, only the deep knowledge of NDM-1 architecture and of the variable mechanism of action that NDM-1 employs against different classes of substrates could orient a successful drug discovery campaign.
Collapse
Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| |
Collapse
|
38
|
Qian X, Zhang S, Xue S, Mao W, Xu M, Xu W, Xie H. A carbapenem-based fluorescence assay for the screening of metallo-β-lactamase inhibitors. Bioorg Med Chem Lett 2019; 29:322-325. [DOI: 10.1016/j.bmcl.2018.11.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
|
39
|
Liu XL, Xiang Y, Chen C, Yang KW. Azolylthioacetamides as potential inhibitors of New Delhi metallo-β-lactamase-1 (NDM-1). J Antibiot (Tokyo) 2018; 72:118-121. [DOI: 10.1038/s41429-018-0121-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/30/2018] [Accepted: 10/21/2018] [Indexed: 11/09/2022]
|
40
|
Tehrani KHME, Martin NI. β-lactam/β-lactamase inhibitor combinations: an update. MEDCHEMCOMM 2018; 9:1439-1456. [PMID: 30288219 PMCID: PMC6151480 DOI: 10.1039/c8md00342d] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022]
Abstract
Antibiotic resistance caused by β-lactamase production continues to present a growing challenge to the efficacy of β-lactams and their role as the most important class of clinically used antibiotics. In response to this threat however, only a handful of β-lactamase inhibitors have been introduced to the market over the past thirty years. The first-generation β-lactamase inhibitors (clavulanic acid, sulbactam and tazobactam) are all β-lactam derivatives and work primarily by inactivating class A and some class C serine β-lactamases. The newer generations of β-lactamase inhibitors including avibactam and vaborbactam are based on non-β-lactam structures and their spectrum of inhibition is extended to KPC as an important class A carbapenemase. Despite these advances several class D and virtually all important class B β-lactamases are resistant to existing inhibitors. The present review provides an overview of recent FDA-approved β-lactam/β-lactamase inhibitor combinations as well as an update on research efforts aimed at the discovery and development of novel β-lactamase inhibitors.
Collapse
Affiliation(s)
- Kamaleddin H M E Tehrani
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
- Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories, Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
| |
Collapse
|
41
|
Kang JS, Zhang AL, Faheem M, Zhang CJ, Ai N, Buynak JD, Welsh WJ, Oelschlaeger P. Virtual Screening and Experimental Testing of B1 Metallo-β-lactamase Inhibitors. J Chem Inf Model 2018; 58:1902-1914. [PMID: 30107123 DOI: 10.1021/acs.jcim.8b00133] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The global rise of metallo-β-lactamases (MBLs) is problematic due to their ability to inactivate most β-lactam antibiotics. MBL inhibitors that could be coadministered with and restore the efficacy of β-lactams are highly sought after. In this study, we employ virtual screening of candidate MBL inhibitors without thiols or carboxylates to avoid off-target effects using the Avalanche software package, followed by experimental validation of the selected compounds. As target enzymes, we chose the clinically relevant B1 MBLs NDM-1, IMP-1, and VIM-2. Among 32 compounds selected from an approximately 1.5 million compound library, 6 exhibited IC50 values less than 40 μM against NDM-1 and/or IMP-1. The most potent inhibitors of NDM-1, IMP-1, and VIM-2 had IC50 values of 19 ± 2, 14 ± 1, and 50 ± 20 μM, respectively. While chemically diverse, the most potent inhibitors all contain combinations of hydroxyl, ketone, ester, amide, or sulfonyl groups. Docking studies suggest that these electron-dense moieties are involved in Zn(II) coordination and interaction with protein residues. These novel scaffolds could serve as the basis for further development of MBL inhibitors. A procedure for renaming NDM-1 residues to conform to the class B β-lactamase (BBL) numbering scheme is also included.
Collapse
Affiliation(s)
- Joon S Kang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States.,Department of Biological Sciences , California State Polytechnic University , Pomona , California 91768-2557 , United States
| | - Antonia L Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Mohammad Faheem
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Charles J Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Ni Ai
- Pharmaceutical Informatics Institute, School of Pharmaceutical Sciences , Zhejiang University , Zhejiang 31005 , People's Republic of China
| | - John D Buynak
- Department of Chemistry , Southern Methodist University , Dallas , Texas 75275-0314 , United States
| | - William J Welsh
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, and Division of Chem Informatics, Biomedical Informatics Shared Resource, Rutgers-Cancer Institute of New Jersey , The State University of New Jersey , Piscataway , New Jersey 08854-8021 , United States
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| |
Collapse
|
42
|
El-Sherief HA, Youssif BG, Abbas Bukhari SN, Abdelazeem AH, Abdel-Aziz M, Abdel-Rahman HM. Synthesis, anticancer activity and molecular modeling studies of 1,2,4-triazole derivatives as EGFR inhibitors. Eur J Med Chem 2018; 156:774-789. [DOI: 10.1016/j.ejmech.2018.07.024] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/05/2018] [Accepted: 07/09/2018] [Indexed: 01/17/2023]
|
43
|
Song GQ, Wang WM, Li ZS, Wang Y, Wang JG. First identification of isatin-β-thiosemicarbazones as novel inhibitors of New Delhi metallo-β-lactamase-1: Chemical synthesis, biological evaluation and molecular simulation. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.09.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
44
|
Fizer M, Slivka M, Mariychuk R, Baumer V, Lendel V. 3-Methylthio-4-phenyl-5-phenylamino-1,2,4-triazole hexabromotellurate:X-ray and computational study. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.054] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
45
|
Wang J, Li Y, Yan H, Duan J, Luo X, Feng X, Lu L, Wang W. Semi-rational screening of the inhibitors and β-lactam antibiotics against the New Delhi metallo-β-lactamase 1 (NDM-1) producing E. coli. RSC Adv 2018; 8:5936-5944. [PMID: 35539612 PMCID: PMC9078263 DOI: 10.1039/c7ra12778b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 02/01/2018] [Indexed: 11/21/2022] Open
Abstract
Bacteria containing bla NDM-1 gene are a growing threat to almost all clinically β-lactam antibiotics. Especially, the New Delhi metallo-β-lactamase (NDM-1) has become a potential public survival risk. In this study, a novel and efficient strategy for inhibitors and β-lactam antibiotics screening using recombinant New Delhi metallo-beta-lactamase (NDM-1) was developed. First, the gene of bla NDM-1 were identified and cloned from multi-drug resistance of Acinetobacter baumannii isolate; by the means of protein expression and purification, recombinant NDM-1 activity was up to 68.5 U ml-1, and high purity NDM-1 protein with activity of 347.4 U mg-1 was obtained. Finally, for NDM-1, the inhibitors (aspergillomarasmine A (AMA) and EDTA) with high affinity (HI) and the β-lactam antibiotics (imipenem) with low affinity (LA) were screened out. Surprisingly, the inhibition of the NDM-1 was enhanced by the use of inhibitor combinations (AMA-EDTA (1 : 2)), where the IC50 of AMA-EDTA was reduced by 88% and 95%, respectively, comparing to the AMA and EDTA alone. More interesting, AMA-EDTA could restore the activity of imipenem when tested against NDM-1 expressing strains (E. coli and Acinetobacter baumannii), with a working time of 120 min and 330 min, respectively. This method is expected to be used in high-throughput screening, drug redesign (including new inhibitors and drugs) and "old drug new use".
Collapse
Affiliation(s)
- Juan Wang
- Laboratory Medicine Department, Zhongshan People's Hospital, The Affiliated Hospital of Sun Yat-Sen University, Guangdong Province No. 2 Sun Wen East Road Zhongshan Guangdong 528403 China
| | - Yang Li
- Laboratory Medicine Department, Zhongshan People's Hospital, The Affiliated Hospital of Sun Yat-Sen University, Guangdong Province No. 2 Sun Wen East Road Zhongshan Guangdong 528403 China
| | - Haizhong Yan
- Laboratory Medicine Department, Zhongshan People's Hospital, The Affiliated Hospital of Sun Yat-Sen University, Guangdong Province No. 2 Sun Wen East Road Zhongshan Guangdong 528403 China
| | - Juan Duan
- Laboratory Medicine Department, Zhongshan People's Hospital, The Affiliated Hospital of Sun Yat-Sen University, Guangdong Province No. 2 Sun Wen East Road Zhongshan Guangdong 528403 China
| | - Xihua Luo
- Laboratory Medicine Department, Zhongshan People's Hospital, The Affiliated Hospital of Sun Yat-Sen University, Guangdong Province No. 2 Sun Wen East Road Zhongshan Guangdong 528403 China
| | - Xueqin Feng
- Laboratory Medicine Department, Zhongshan People's Hospital, The Affiliated Hospital of Sun Yat-Sen University, Guangdong Province No. 2 Sun Wen East Road Zhongshan Guangdong 528403 China
| | - Lanfen Lu
- Laboratory Medicine Department, Zhongshan People's Hospital, The Affiliated Hospital of Sun Yat-Sen University, Guangdong Province No. 2 Sun Wen East Road Zhongshan Guangdong 528403 China
| | - Weijia Wang
- Laboratory Medicine Department, Zhongshan People's Hospital, The Affiliated Hospital of Sun Yat-Sen University, Guangdong Province No. 2 Sun Wen East Road Zhongshan Guangdong 528403 China
| |
Collapse
|
46
|
Liu S, Jing L, Yu ZJ, Wu C, Zheng Y, Zhang E, Chen Q, Yu Y, Guo L, Wu Y, Li GB. (( S )-3-Mercapto-2-methylpropanamido)acetic acid derivatives as metallo-β-lactamase inhibitors: Synthesis, kinetic and crystallographic studies. Eur J Med Chem 2018; 145:649-660. [DOI: 10.1016/j.ejmech.2018.01.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
|
47
|
Docquier JD, Mangani S. An update on β-lactamase inhibitor discovery and development. Drug Resist Updat 2017; 36:13-29. [PMID: 29499835 DOI: 10.1016/j.drup.2017.11.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 11/27/2022]
Abstract
Antibiotic resistance, and the emergence of pan-resistant clinical isolates, seriously threatens our capability to treat bacterial diseases, including potentially deadly hospital-acquired infections. This growing issue certainly requires multiple adequate responses, including the improvement of both diagnosis methods and use of antibacterial agents, and obviously the development of novel antibacterial drugs, especially active against Gram-negative pathogens, which represent an urgent medical need. Considering the clinical relevance of both β-lactam antibiotics and β-lactamase-mediated resistance, the discovery and development of combinations including a β-lactamase inhibitor seems to be particularly attractive, despite being extremely challenging due to the enormous diversity, both structurally and mechanistically, of the potential β-lactamase targets. This review will cover the evolution of currently available β-lactamase inhibitors along with the most recent research leading to new β-lactamase inhibitors of potential clinical interest or already in the stage of clinical development.
Collapse
Affiliation(s)
- Jean-Denis Docquier
- Department of Medical Biotechnology, University of Siena, Viale Bracci 16, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| |
Collapse
|
48
|
Xiang Y, Chang YN, Ge Y, Kang JS, Zhang YL, Liu XL, Oelschlaeger P, Yang KW. Azolylthioacetamides as a potent scaffold for the development of metallo-β-lactamase inhibitors. Bioorg Med Chem Lett 2017; 27:5225-5229. [PMID: 29122480 DOI: 10.1016/j.bmcl.2017.10.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/18/2017] [Accepted: 10/19/2017] [Indexed: 11/29/2022]
Abstract
In an effort to develop new inhibitors of metallo-β-lactamases (MβLs), twenty-eight azolylthioacetamides were synthesized and assayed against MβLs. The obtained benzimidazolyl and benzioxazolyl substituted 1-19 specifically inhibited the enzyme ImiS, and 10 was found to be the most potent inhibitor of ImiS with an IC50 value of 15 nM. The nitrobenzimidazolyl substituted 20-28 specifically inhibited NDM-1, with 27 being the most potent inhibitor with an IC50 value of 170 nM. Further studies with 10, 11, and 27 revealed a mixed inhibition mode with competitive and uncompetitive inhibition constants in a similar range as the IC50 values. These inhibitors resulted in a 2-4-fold decrease in imipenem MIC values using E. coli cells producing ImiS or NDM-1. While the source of uncompetitive (possibly allosteric) inhibition remains unclear, docking studies indicate that 10 and 11 may interact orthosterically with Zn2 in the active site of CphA, while 27 could bridge the two Zn(II) ions in the active site of NDM-1 via its nitro group.
Collapse
Affiliation(s)
- Yang Xiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ya-Nan Chang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ying Ge
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Joon S Kang
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Yi-Lin Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Xiao-Long Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
| |
Collapse
|
49
|
Inhibitors of metallo-β-lactamases. Curr Opin Microbiol 2017; 39:96-105. [DOI: 10.1016/j.mib.2017.10.026] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/09/2017] [Accepted: 10/28/2017] [Indexed: 11/19/2022]
|
50
|
Sadaf A, Sinha R, Khare SK. Structure and Functional Characterisation of a Distinctive β-Lactamase from an Environmental Strain EMB20 of Bacillus cereus. Appl Biochem Biotechnol 2017; 184:197-211. [PMID: 28664525 DOI: 10.1007/s12010-017-2539-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/14/2017] [Indexed: 11/30/2022]
Abstract
The rampant use and misuse of antibiotics in human medicine, agriculture and veterinary have become the key contributors to global antimicrobial resistance. One of the significant resistance mechanisms that inactivates antibiotics and impedes treatment of bacterial infections is the expression of β-lactamases. Rising evidence of newer variants of β-lactamases in the environment is therefore a serious threat to the presently available antibiotic armoury. The present work describes the purification of a variant β-lactamase isolated from a soil strain EMB20 of Bacillus cereus. The lactamase was purified using three-phase partitioning and gel filtration chromatography to a 30-fold purification and 15% recovery yield. Contrary to the general trend, the lactamase was not a metalloenzyme, but its activity was enhanced in the presence of Mg2+ and Mn2+. The EMB20 lactamase exhibited improved stability against inhibitors and denaturing agents such as urea and GdmCl as compared to its commercial analogue. The improved stability of EMB20 lactamase was further validated by circular dichroism and fluorescence spectroscopy. This study reemphasizes the rising prevalence of environmental lactamase variants. Decoding the structure-function correlation of such lactamases in the presence of inhibitors will provide insights into the response of this enzyme towards inhibitors as well as its substrates.
Collapse
Affiliation(s)
- Ayesha Sadaf
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Rajeshwari Sinha
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - S K Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
| |
Collapse
|