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Gong Y, Feng Y, Lv X. Identification of a Novel KPC Variant, KPC-204, Conferring Resistance to Both Carbapenems and Ceftazidime-Avibactam in an ST11 Klebsiella pneumoniae Strain. Microorganisms 2024; 12:1193. [PMID: 38930575 PMCID: PMC11205768 DOI: 10.3390/microorganisms12061193] [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: 05/22/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
This study describes KPC-204, a novel variant of Klebsiella pneumoniae carbapenemase, characterized by a Lys-Asp-Asp (KDD) amino acid insertion at Ambler position 269 deviates from KPC-2. This variant was identified in an ST11-type clinical isolate of carbapenem-resistant Klebsiella pneumoniae from China. Notably, KPC-204 exhibits resistance to both ceftazidime-avibactam and carbapenems. Genetic analysis revealed that blaKPC-204 was located on a highly mobile IncFII/IncR plasmid within a complex genetic structure that facilitates its spread. Functional analysis, achieved through cloning into E. coli DH5α, validates KPC-204's contribution to increased resistance to ceftazidime-avibactam. The kinetic parameters showed that KPC-204 exhibited similar affinity to KPC-2 toward ceftazidime and reduced sensitivity to avibactam. Docking simulations revealed a weaker interaction between KPC-204 and avibactam compared to KPC-2. Mating experiments demonstrated the resistance's transmissibility. This investigation underscores the evolving diversity of KPC variants affecting ceftazidime-avibactam resistance, highlighting the necessity for continuous monitoring.
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Affiliation(s)
- Yanqiao Gong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.G.); (Y.F.)
- Department of Infection Control, Minda Hospital, Hubei Minzu University, Enshi 445000, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.G.); (Y.F.)
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoju Lv
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.G.); (Y.F.)
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu 610041, China
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2
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Yan YH, Zhang TT, Li R, Wang SY, Wei LL, Wang XY, Zhu KR, Li SR, Liang GQ, Yang ZB, Yang LL, Qin S, Li GB. Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-β-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding. J Med Chem 2023; 66:13746-13767. [PMID: 37791640 DOI: 10.1021/acs.jmedchem.3c01189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Metallo-β-lactamases (MBLs) are zinc-dependent enzymes capable of hydrolyzing all bicyclic β-lactam antibiotics, posing a great threat to public health. However, there are currently no clinically approved MBL inhibitors. Despite variations in their active sites, MBLs share a common catalytic mechanism with carbapenems, forming similar reaction species and hydrolysates. We here report the development of 2-aminothiazole-4-carboxylic acids (AtCs) as broad-spectrum MBL inhibitors by mimicking the anchor pharmacophore features of carbapenem hydrolysate binding. Several AtCs manifested potent activity against B1, B2, and B3 MBLs. Crystallographic analyses revealed a common binding mode of AtCs with B1, B2, and B3 MBLs, resembling binding observed in the MBL-carbapenem product complexes. AtCs restored Meropenem activity against MBL-producing isolates. In the murine sepsis model, AtCs exhibited favorable synergistic efficacy with Meropenem, along with acceptable pharmacokinetics and safety profiles. This work offers promising lead compounds and a structural basis for the development of potential drug candidates to combat MBL-mediated antimicrobial resistance.
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Affiliation(s)
- Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ting-Ting Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, China
| | - Rong Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Si-Yao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Liu-Liu Wei
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xin-Yue Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Kai-Rong Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shan-Rui Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Guo-Qing Liang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Zeng-Bao Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ling-Ling Yang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, China
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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3
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Yan YH, Ding HS, Zhu KR, Mu BS, Zheng Y, Huang MY, Zhou C, Li WF, Wang Z, Wu Y, Li GB. Metal binding pharmacophore click-derived discovery of new broad-spectrum metallo-β-lactamase inhibitors. Eur J Med Chem 2023; 257:115473. [PMID: 37209449 DOI: 10.1016/j.ejmech.2023.115473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 05/22/2023]
Abstract
The emergence of metallo-β-lactamases (MBLs) confers resistance to nearly all the β-lactam antibiotics, including carbapenems. Currently, there is a lack of clinically useful MBL inhibitors, making it crucial to discover new inhibitor chemotypes that can potently target multiple clinically relevant MBLs. Herein we report a strategy that utilizes a metal binding pharmacophore (MBP) click approach to identify new broad-spectrum MBL inhibitors. Our initial investigation identified several MBPs including phthalic acid, phenylboronic acid and benzyl phosphoric acid, which were subjected to structural transformations using azide-alkyne click reactions. Subsequent structure-activity relationship analyses led to the identification of several potent broad-spectrum MBL inhibitors, including 73 that manifested IC50 values ranging from 0.00012 μM to 0.64 μM against multiple MBLs. Co-crystallographic studies demonstrated the importance of MBPs in engaging with the MBL active site anchor pharmacophore features, and revealed the unusual two-molecule binding modes with IMP-1, highlighting the critical role of flexible active site loops in recognizing structurally diverse substrates/inhibitors. Our work provides new chemotypes for MBL inhibition and establishes a MBP click-derived paradigm for inhibitor discovery targeting MBLs as well as other metalloenzymes.
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Affiliation(s)
- Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Hao-Sheng Ding
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Kai-Rong Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Bin-Song Mu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yang Zheng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Meng-Yi Huang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Cong Zhou
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Wen-Fang Li
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhenling Wang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yong Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
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4
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A modified bonded model approach for molecular dynamics simulations of New Delhi Metallo-β-lactamase. J Mol Graph Model 2023; 121:108431. [PMID: 36827734 DOI: 10.1016/j.jmgm.2023.108431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
Modelling metalloproteins using the classical force fields is challenging. Several methods have been devised to model metalloproteins in force fields. Of these methods, the bonded model, combined with Restrained Electrostatic Potential (RESP) charge fitting, proved its superiority. The latter method was facilitated by the development of the python-based Metal Centre Parameter Builder (MCPB.py) AmberTool. However, the standard bonded model method offered by the MCPB.py tool may not be appropriate for validating and refining the binding modes predicted by docking when crystal structures are lacking. That is because the representation of coordination interactions between any bound ligand and metal ions by covalent bonds can hinder the flexibility of the ligand. Therefore, a new modification to the standard bonded model approach is proposed here. Molecular dynamics (MD) simulations based on the new modified bonded model (MBM) approach avoid the bias caused by coordination bonds and, unlike hybrid QM/MM MD, allow for sufficient sampling of the binding mode given the currently available computational power. The MBM MD approach reproduced the studied crystal structure conformations of New Delhi Metallo-β-lactamase 1 (NDM-1). Furthermore, the MBM approach described the binding interactions of intact β-lactams with NDM-1 reasonably, and predicted a non-productive binding mode for the poor NDM-1 substrate aztreonam whilst predicting productive binding modes for known good substrates. This study presents a useful MD method for metallo-β-lactamases and provides better understanding of β-lactam substrates recognition by NDM-1. The proposed MBM approach might also be useful in the investigation of other metal-containing protein targets.
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5
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Design, Synthesis, and Biological Evaluation of New 1H-Imidazole-2-Carboxylic Acid Derivatives as Metallo-β-Lactamase Inhibitors. Bioorg Med Chem 2022; 72:116993. [PMID: 36084491 DOI: 10.1016/j.bmc.2022.116993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/21/2022]
Abstract
As one of important mechanisms to β-lactam antimicrobial resistance, metallo-β-lactamases (MBLs) have been receiving increasing worldwide attentions. Ambler subclass B1 MBLs are most clinically relevant, because they can hydrolyze almost all β-lactams with the exception of monobactams. However, it is still lacking of clinically useful drugs to combat MBL-medicated resistance. We previously identified 1H-imidazole-2-carboxylic acid as a core metal-binding pharmacophore (MBP) to target multiple B1 MBLs. Herein, we report structural optimization of 1H-imidazole-2-carboxylic acid and substituents. Structure-activity relationship (SAR) analyses revealed that replacement of 1H-imidazole-2-carboxylic acid with other structurally highly similar MBPs excepting thiazole-4-carboxylic acid resulted in decreased MBL inhibition. Further SAR studies identified more potent inhibitors to MBLs, of which 28 manifested IC50 values of 0.018 µM for both VIM-2 and VIM-5. The microbiological tests demonstrated that the most tested compounds showed improved synergistic effects; some compounds at 1 µg/ml were able to reduce meropenem MIC by at least 16-fold, which will be worth further development of new potent inhibitors particularly targeting VIM-type MBLs.
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6
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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.
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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.
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7
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The development of New Delhi metallo-β-lactamase-1 inhibitors since 2018. Microbiol Res 2022; 261:127079. [DOI: 10.1016/j.micres.2022.127079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022]
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8
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Methimazole and α-lipoic acid as metallo-β-lactamases inhibitors. J Antibiot (Tokyo) 2022; 75:282-286. [PMID: 35197545 DOI: 10.1038/s41429-022-00513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/26/2022] [Accepted: 01/30/2022] [Indexed: 11/08/2022]
Abstract
The emergence of bacterial resistance poses a serious threat to public health. One of the most important resistance mechanisms against β-lactam antibiotics is the production of metallo-β-lactamases (MBLs). In this study, α-lipoic acid (LA) and methimazole (MMI), which have been used in clinical practice as non-antibacterial drugs and as a supplement, were chosen to explore their potential to be metallo-β-lactamases inhibitors (MBLIs). Enzyme inhibition assays showed that LA and MMI had moderate inhibitory activity against NDM-1 but no activity against VIM-2 and IMP-7. Antibacterial assays to determine synergy, demonstrated that the combination of LA or MMI with meropenem (MER) reduced the MIC value of MER against NDM-1 producing E. coli 16 times and 4 times, respectively, lower than that of MER alone. The fractional inhibitory concentration index (FICI) values were calculated to be less than 0.5, indicating that both LA and MMI had synergistic antibacterial effects with MER against all three MBLs expressing E. coli strains. The time-kill studies also suggested that LA and MMI were effective in restoring the antibacterial effect of MER. These findings revealed that LA and MMI are potential carbapenem enhancers, and provide a starting point for the development of potent MBLIs.
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Grigorenko VG, Khrenova MG, Andreeva IP, Rubtsova MY, Lev AI, Novikova TS, Detusheva EV, Fursova NK, Dyatlov IA, Egorov AM. Drug Repurposing of the Unithiol: Inhibition of Metallo-β-Lactamases for the Treatment of Carbapenem-Resistant Gram-Negative Bacterial Infections. Int J Mol Sci 2022; 23:ijms23031834. [PMID: 35163756 PMCID: PMC8837113 DOI: 10.3390/ijms23031834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 02/05/2023] Open
Abstract
The increasing antibiotic resistance is a clinical problem worldwide. Numerous Gram-negative bacteria have already become resistant to the most widely used class of antibacterial drugs, β-lactams. One of the main mechanisms is inactivation of β-lactam antibiotics by bacterial β-lactamases. Appearance and spread of these enzymes represent a continuous challenge for the clinical treatment of infections and for the design of new antibiotics and inhibitors. Drug repurposing is a prospective approach for finding new targets for drugs already approved for use. We describe here the inhibitory potency of known detoxifying antidote 2,3-dimercaptopropane-1-sulfonate (unithiol) against metallo-β-lactamases. Unithiol acts as a competitive inhibitor of meropenem hydrolysis by recombinant metallo-β-lactamase NDM-1 with the KI of 16.7 µM. It is an order of magnitude lower than the KI for l-captopril, the inhibitor of angiotensin-converting enzyme approved as a drug for the treatment of hypertension. Phenotypic methods demonstrate that the unithiol inhibits natural metallo-β-lactamases NDM-1 and VIM-2 produced by carbapenem-resistant K. pneumoniae and P. aeruginosa bacterial strains. The 3D full atom structures of unithiol complexes with NDM-1 and VIM-2 are obtained using QM/MM modeling. The thiol group is located between zinc cations of the active site occupying the same place as the catalytic hydroxide anion in the enzyme–substrate complex. The sulfate group forms both a coordination bond with a zinc cation and hydrogen bonds with the positively charged residue, lysine or arginine, responsible for proper orientation of antibiotics upon binding to the active site prior to hydrolysis. Thus, we demonstrate both experimentally and theoretically that the unithiol is a prospective competitive inhibitor of metallo-β-lactamases and it can be utilized in complex therapy together with the known β-lactam antibiotics.
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Affiliation(s)
- Vitaly G. Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
- Correspondence: (V.G.G.); (M.G.K.)
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence: (V.G.G.); (M.G.K.)
| | - Irina P. Andreeva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
| | - Maya Yu. Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
| | - Anastasia I. Lev
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Tatiana S. Novikova
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Elena V. Detusheva
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Nadezhda K. Fursova
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Ivan A. Dyatlov
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Alexey M. Egorov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
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1,2,4-Triazole-3-thione compounds with a 4-ethyl alkyl/aryl sulfide substituent are broad-spectrum metallo-β-lactamase inhibitors with re-sensitization activity. Eur J Med Chem 2021; 226:113873. [PMID: 34626878 DOI: 10.1016/j.ejmech.2021.113873] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023]
Abstract
Metallo-β-lactamases (MBLs) are important contributors of Gram-negative bacteria resistance to β-lactam antibiotics. MBLs are highly worrying because of their carbapenemase activity, their rapid spread in major human opportunistic pathogens while no clinically useful inhibitor is available yet. In this context, we are exploring the potential of compounds based on the 1,2,4-triazole-3-thione scaffold as an original ligand of the di-zinc active sites of MBLs, and diversely substituted at its positions 4 and 5. Here, we present a new series of compounds substituted at the 4-position by a thioether-containing alkyl chain with a carboxylic and/or an aryl group at its extremity. Several compounds showed broad-spectrum inhibition with Ki values in the μM to sub-μM range against VIM-type enzymes, NDM-1 and IMP-1. The presence of the sulfur and of the aryl group was important for the inhibitory activity and the binding mode of a few compounds in VIM-2 was revealed by X-ray crystallography. Importantly, in vitro antibacterial susceptibility assays showed that several inhibitors were able to potentiate the activity of meropenem on Klebsiella pneumoniae clinical isolates producing VIM-1 or VIM-4, with a potentiation effect of up to 16-fold. Finally, a selected compound was found to only moderately inhibit the di-zinc human glyoxalase II, and several showed no or only moderate toxicity toward several human cells, thus favourably completing a promising behaviour.
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11
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Yan YH, Li W, Chen W, Li C, Zhu KR, Deng J, Dai QQ, Yang LL, Wang Z, Li GB. Structure-guided optimization of 1H-imidazole-2-carboxylic acid derivatives affording potent VIM-Type metallo-β-lactamase inhibitors. Eur J Med Chem 2021; 228:113965. [PMID: 34763944 DOI: 10.1016/j.ejmech.2021.113965] [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: 09/14/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023]
Abstract
Production of metallo-β-lactamases (MBLs) in bacterial pathogens is an important cause of resistance to the 'last-resort' carbapenem antibiotics. Development of effective MBL inhibitors to reverse carbapenem resistance in Gram-negative bacteria is still needed. We herein report X-ray structure-guided optimization of 1H-imidazole-2-carboxylic acid (ICA) derivatives by considering how to engage with the active-site flexible loops and improve penetration into Gram-negative bacteria. Structure-activity relationship studies revealed the importance of appropriate substituents at ICA 1-position to achieve potent inhibition to class B1 MBLs, particularly the Verona Integron-encoded MBLs (VIMs), mainly by involving ingenious interactions with the flexible active site loops as observed by crystallographic analyses. Of the tested ICA inhibitors, 55 displayed potent synergistic antibacterial activity with meropenem against engineered Escherichia coli strains and even intractable clinically isolated Pseudomonas aeruginosa producing VIM-2 MBL. The morphologic and internal structural changes of bacterial cells after treatment further demonstrated that 55 crossed the outer membrane and reversed the activity of meropenem. Moreover, 55 showed good pharmacokinetic and safety profile in vivo, which could be a potential candidate for combating VIM-mediated Gram-negative carbapenem resistance.
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Affiliation(s)
- Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China
| | - Wenfang Li
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wei Chen
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, China
| | - Chao Li
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, China
| | - Kai-Rong Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China
| | - Ji Deng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China
| | - Qing-Qing Dai
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China
| | - Ling-Ling Yang
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, China
| | - Zhenling Wang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China.
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12
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Yahiaoui S, Voos K, Haupenthal J, Wichelhaus TA, Frank D, Weizel L, Rotter M, Brunst S, Kramer JS, Proschak E, Ducho C, Hirsch AKH. N-Aryl mercaptoacetamides as potential multi-target inhibitors of metallo-β-lactamases (MBLs) and the virulence factor LasB from Pseudomonas aeruginosa. RSC Med Chem 2021; 12:1698-1708. [PMID: 34778771 PMCID: PMC8528214 DOI: 10.1039/d1md00187f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/23/2021] [Indexed: 12/18/2022] Open
Abstract
Increasing antimicrobial resistance is evolving to be one of the major threats to public health. To reduce the selection pressure and thus to avoid a fast development of resistance, novel approaches aim to target bacterial virulence instead of growth. Another strategy is to restore the activity of antibiotics already in clinical use. This can be achieved by the inhibition of resistance factors such as metallo-β-lactamases (MBLs). Since MBLs can cleave almost all β-lactam antibiotics, including the “last resort” carbapenems, their inhibition is of utmost importance. Here, we report on the synthesis and in vitro evaluation of N-aryl mercaptoacetamides as inhibitors of both clinically relevant MBLs and the virulence factor LasB from Pseudomonas aeruginosa. All tested N-aryl mercaptoacetamides showed low micromolar to submicromolar activities on the tested enzymes IMP-7, NDM-1 and VIM-1. The two most promising compounds were further examined in NDM-1 expressing Klebsiella pneumoniae isolates, where they restored the full activity of imipenem. Together with their LasB-inhibitory activity in the micromolar range, this class of compounds can now serve as a starting point for a multi-target inhibitor approach against both bacterial resistance and virulence, which is unprecedented in antibacterial drug discovery. Simultaneous inhibition of metallo-β-lactamases (MBLs) and virulence factors such as LasB from Pseudomonas aeruginosa offers a new approach to combat antibiotic-resistant pathogens.![]()
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Affiliation(s)
- Samir Yahiaoui
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Katrin Voos
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt Paul-Ehrlich-Straße 40 60596 Frankfurt Germany
| | - Denia Frank
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt Paul-Ehrlich-Straße 40 60596 Frankfurt Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Marco Rotter
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University Campus Building E8 1 66123 Saarbrücken Germany
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13
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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.
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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
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14
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Egorov AM, Ulyashova MM, Rubtsova MY. Inhibitors of β-Lactamases. New Life of β-Lactam Antibiotics. BIOCHEMISTRY (MOSCOW) 2021; 85:1292-1309. [PMID: 33280574 DOI: 10.1134/s0006297920110024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
β-Lactam antibiotics account for about 60% of all produced antibiotics. Due to a high activity and minimal side effects, they are the most commonly used class of antibacterial drugs for the treatment of various infectious diseases of humans and animals, including severe hospital infections. However, the emergence of bacteria resistant to β-lactams has led to the clinical inefficiency of these antibiotics, and as a result, their use in medicine has been limited. The search for new effective ways for overcoming the resistance to β-lactam antibiotics is an essential task. The major mechanism of bacterial resistance is the synthesis of β-lactamases (BLs) that break the antibiotic β-lactam ring. Here, we review specific inhibitors of serine β-lactamases and metallo-β-lactamases and discuss approaches for creating new inhibitors that would prolong the "life" of β-lactams.
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Affiliation(s)
- A M Egorov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - M M Ulyashova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - M Yu Rubtsova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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15
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Dai Q, Yan Y, Ning X, Li G, Yu J, Deng J, Yang L, Li GB. AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo- β-lactamases and indoleamine/tryptophan 2,3-dioxygenases. Acta Pharm Sin B 2021; 11:1931-1946. [PMID: 34386329 PMCID: PMC8343198 DOI: 10.1016/j.apsb.2021.01.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/25/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022] Open
Abstract
We herein describe AncPhore, a versatile tool for drug discovery, which is characterized by pharmacophore feature analysis and anchor pharmacophore (i.e., most important pharmacophore features) steered molecular fitting and virtual screening. Comparative analyses of numerous protein–ligand complexes using AncPhore revealed that anchor pharmacophore features are biologically important, commonly associated with protein conservative characteristics, and have significant contributions to the binding affinity. Performance evaluation of AncPhore showed that it had substantially improved prediction ability on different types of target proteins including metalloenzymes by considering the specific contributions and diversity of anchor pharmacophore features. To demonstrate the practicability of AncPhore, we screened commercially available chemical compounds and discovered a set of structurally diverse inhibitors for clinically relevant metallo-β-lactamases (MBLs); of them, 4 and 6 manifested potent inhibitory activity to VIM-2, NDM-1 and IMP-1 MBLs. Crystallographic analyses of VIM-2:4 complex revealed the precise inhibition mode of 4 with VIM-2, highly consistent with the defined anchor pharmacophore features. Besides, we also identified new hit compounds by using AncPhore for indoleamine/tryptophan 2,3-dioxygenases (IDO/TDO), another class of clinically relevant metalloenzymes. This work reveals anchor pharmacophore as a valuable concept for target-centered drug discovery and illustrates the potential of AncPhore to efficiently identify new inhibitors for different types of protein targets.
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Key Words
- AMPC, asian mouse phenotyping consortium
- AP, anchor pharmacophore
- AR, aromatic ring
- AUC, area under the curve
- Anchor pharmacophore
- BACE1, beta-secretase 1
- BRD4, bromodomain-containing protein 4
- CA, carbonic anhydrase
- CA2, carbonic anhydrase 2
- CDK2, cyclin-dependent kinase 2
- CTS, cathepsins
- CV, covalent bonding
- CatK, cathepsin K
- EF, enrichment factor
- EX, exclusion volume
- GA, genetic algorithm
- HA, hydrogen-bond acceptor
- HD, hydrogen-bond donor
- HIV-P, human immunodeficiency virus protease
- HIV1-P, human immunodeficiency virus type 1 protease
- HY, hydrophobic
- IDO1, indoleamine 2,3-dioxygenase 1
- IMP, imipenemase
- Indoleamine 2,3-dioxygenase
- LE, ligand efficiency
- MAPK14, mitogen-activated protein kinase 14
- MB, metal coordination
- MBL, metallo-β-lactamase
- MIC, minimum inhibitory concentration
- MMP, matrix metalloproteinase
- MMP13, matrix metallopeptidase 13
- Metallo-β-lactamase
- Metalloenzyme
- NDM, new delhi MBL
- NE, negatively charged center
- NP, without anchor pharmacophore features
- PO, positively charged center
- RMSD, root mean square deviation
- ROC curve, receiver operating characteristic curve
- ROCK1, rho-associated protein kinase 1
- RT, reverse transcriptase
- RTK, receptor tyrosine kinase
- SBL, serine beta lactamase
- SSEL, secondary structure element length
- STK, serine threonine kinase
- TDO, tryptophan 2,3-dioxygenase
- TDSS, torsion-driving systematic search
- TNKS2, tankyrase 2
- Tryptophan 2,3-dioxygenase
- VEGFR2, vascular endothelial growth factor receptor 2
- VIM, verona integron-encoded MBL
- Virtual screening
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16
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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.
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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.
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17
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Ning XL, Li YZ, Huo C, Deng J, Gao C, Zhu KR, Wang M, Wu YX, Yu JL, Ren YL, Luo ZY, Li G, Chen Y, Wang SY, Peng C, Yang LL, Wang ZY, Wu Y, Qian S, Li GB. X-ray Structure-Guided Discovery of a Potent, Orally Bioavailable, Dual Human Indoleamine/Tryptophan 2,3-Dioxygenase (hIDO/hTDO) Inhibitor That Shows Activity in a Mouse Model of Parkinson's Disease. J Med Chem 2021; 64:8303-8332. [PMID: 34110158 DOI: 10.1021/acs.jmedchem.1c00303] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human indoleamine 2,3-dioxygenase 1 (hIDO1) and tryptophan 2,3-dioxygenase (hTDO) have been closely linked to the pathogenesis of Parkinson's disease (PD); nevertheless, development of dual hIDO1 and hTDO inhibitors to evaluate their potential efficacy against PD is still lacking. Here, we report biochemical, biophysical, and computational analyses revealing that 1H-indazole-4-amines inhibit both hIDO1 and hTDO by a mechanism involving direct coordination with the heme ferrous and ferric states. Crystal structure-guided optimization led to 23, which manifested IC50 values of 0.64 and 0.04 μM to hIDO1 and hTDO, respectively, and had good pharmacokinetic properties and brain penetration in mice. 23 showed efficacy against the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse motor coordination deficits, comparable to Madopar, an anti-PD medicine. Further studies revealed that different from Madopar, 23 likely has specific anti-PD mechanisms involving lowering IDO1 expression, alleviating dopaminergic neurodegeneration, reducing inflammatory cytokines and quinolinic acid in mouse brain, and increasing kynurenic acid in mouse blood.
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MESH Headings
- 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine
- Animals
- Brain/pathology
- Cell Line, Tumor
- Crystallography, X-Ray
- Enzyme Inhibitors/chemical synthesis
- Enzyme Inhibitors/metabolism
- Enzyme Inhibitors/therapeutic use
- Humans
- Indazoles/chemical synthesis
- Indazoles/metabolism
- Indazoles/therapeutic use
- Indoleamine-Pyrrole 2,3,-Dioxygenase/antagonists & inhibitors
- Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism
- Male
- Mice, Inbred C57BL
- Molecular Docking Simulation
- Molecular Structure
- Neuroprotective Agents/chemical synthesis
- Neuroprotective Agents/metabolism
- Neuroprotective Agents/therapeutic use
- Parkinson Disease, Secondary/chemically induced
- Parkinson Disease, Secondary/drug therapy
- Parkinson Disease, Secondary/pathology
- Protein Binding
- Structure-Activity Relationship
- Tryptophan Oxygenase/antagonists & inhibitors
- Tryptophan Oxygenase/metabolism
- Mice
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Affiliation(s)
- Xiang-Li Ning
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yu-Zhi Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Cui Huo
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Ji Deng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Cheng Gao
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Kai-Rong Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Miao Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yu-Xiang Wu
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Jun-Lin Yu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ya-Li Ren
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zong-Yuan Luo
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Gen Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yang Chen
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Si-Yao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ling-Ling Yang
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Zhou-Yu Wang
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yong Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shan Qian
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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18
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Discovery of 3-aryl substituted benzoxaboroles as broad-spectrum inhibitors of serine- and metallo-β-lactamases. Bioorg Med Chem Lett 2021; 41:127956. [DOI: 10.1016/j.bmcl.2021.127956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/26/2021] [Accepted: 03/07/2021] [Indexed: 11/22/2022]
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19
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Romero E, Oueslati S, Benchekroun M, D'Hollander ACA, Ventre S, Vijayakumar K, Minard C, Exilie C, Tlili L, Retailleau P, Zavala A, Elisée E, Selwa E, Nguyen LA, Pruvost A, Naas T, Iorga BI, Dodd RH, Cariou K. Azetidinimines as a novel series of non-covalent broad-spectrum inhibitors of β-lactamases with submicromolar activities against carbapenemases KPC-2 (class A), NDM-1 (class B) and OXA-48 (class D). Eur J Med Chem 2021; 219:113418. [PMID: 33862516 DOI: 10.1016/j.ejmech.2021.113418] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022]
Abstract
The occurrence of resistances in Gram negative bacteria is steadily increasing to reach extremely worrying levels and one of the main causes of resistance is the massive spread of very efficient β-lactamases which render most β-lactam antibiotics useless. Herein, we report the development of a series of imino-analogues of β-lactams (namely azetidinimines) as efficient non-covalent inhibitors of β-lactamases. Despite the structural and mechanistic differences between serine-β-lactamases KPC-2 and OXA-48 and metallo-β-lactamase NDM-1, all three enzymes can be inhibited at a submicromolar level by compound 7dfm, which can also repotentiate imipenem against a resistant strain of Escherichia coli expressing NDM-1. We show that 7dfm can efficiently inhibit not only the three main clinically-relevant carbapenemases of Ambler classes A (KPC-2), B (NDM-1) and D (OXA-48) with Ki's below 0.3 μM, but also the cephalosporinase CMY-2 (class C, 86% inhibition at 10 μM). Our results pave the way for the development of a new structurally original family of non-covalent broad-spectrum inhibitors of β-lactamases.
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Affiliation(s)
- Eugénie Romero
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Saoussen Oueslati
- U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Mohamed Benchekroun
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Agathe C A D'Hollander
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Sandrine Ventre
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Kamsana Vijayakumar
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Corinne Minard
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Cynthia Exilie
- U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Linda Tlili
- U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Pascal Retailleau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Agustin Zavala
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France; U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Eddy Elisée
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Edithe Selwa
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Laetitia A Nguyen
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour La Santé, Gif-sur-Yvette, France
| | - Alain Pruvost
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour La Santé, Gif-sur-Yvette, France
| | - Thierry Naas
- U1184, Inserm, Université Paris-Saclay, LabEx LERMIT, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; EERA Unit "Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-AP-HP-Université Paris-Saclay, Paris, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France.
| | - Robert H Dodd
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France
| | - Kevin Cariou
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, LabEx LERMIT, UPR 2301, Gif-sur-Yvette, France.
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20
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Li JQ, Sun LY, Jiang Z, Chen C, Gao H, Chigan JZ, Ding HH, Yang KW. Diaryl-substituted thiosemicarbazone: A potent scaffold for the development of New Delhi metallo-β-lactamase-1 inhibitors. Bioorg Chem 2020; 107:104576. [PMID: 33383326 DOI: 10.1016/j.bioorg.2020.104576] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 12/15/2022]
Abstract
The superbug infection caused by New Delhi metallo-β-lactamase (NDM-1) has become an emerging public health threat. Inhibition of NDM-1 has proven challenging due to its shuttling between pathogenic bacteria. A potent scaffold, diaryl-substituted thiosemicarbazone, was constructed and assayed with metallo-β-lactamases (MβLs). The obtained twenty-six molecules specifically inhibited NDM-1 with IC50 0.038-34.7 µM range (except 1e, 2e, and 3d), and 1c is the most potent inhibitor (IC50 = 0.038 µM). The structure-activity relationship of synthetic thiosemicarbazones revealed that the diaryl-substitutes, specifically 2-pyridine and 2-hydroxylbenzene improved inhibitory activities of the inhibitors. The thiosemicarbazones exhibited synergistic antimycobacterial actions against E. coli-NDM-1, resulted a 2-512-fold reduction in MIC of meropenem, while 1c restored 16-256-, 16-, and 2-fold activity of the antibiotic on clinical isolates ECs, K. pneumonia and P. aeruginosa harboring NDM-1, respectively. Also, mice experiments showed that 1c had a synergistic antibacterial ability with meropenem, reduced the bacterial load clinical isolate EC08 in the spleen and liver. This work provided a highly promising scaffold for the development of NDM-1 inhibitors.
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Affiliation(s)
- 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
| | - 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
| | - Zhihui Jiang
- Department of Pharmacy, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, 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
| | - 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
| | - 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.
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21
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Yang Y, Guo Y, Zhou Y, Gao Y, Wang X, Wang J, Niu X. Discovery of a Novel Natural Allosteric Inhibitor That Targets NDM-1 Against Escherichia coli. Front Pharmacol 2020; 11:581001. [PMID: 33123013 PMCID: PMC7566295 DOI: 10.3389/fphar.2020.581001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/07/2020] [Indexed: 11/25/2022] Open
Abstract
At present, the resistance of New Delhi metallo-β-lactamase-1 (NDM-1) to carbapenems and cephalosporins, one of the mechanisms of bacterial resistance against β-lactam antibiotics, poses a threat to human health. In this work, based on the virtual ligand screen method, we found that carnosic acid (CA), a natural compound, exhibited a significant inhibitory effect against NDM-1 (IC50 = 27.07 μM). Although carnosic acid did not display direct antibacterial activity, the combination of carnosic acid and meropenem still showed bactericidal activity after the loss of bactericidal effect of meropenem. The experimental results showed that carnosic acid can enhance the antibacterial activity of meropenem against Escherichia coli ZC-YN3. To explore the inhibitory mechanism of carnosic acid against NDM-1, we performed the molecular dynamics simulation and binding energy calculation for the NDM-1-CA complex system. Notably, the 3D structure of the complex obtained from molecular modeling indicates that the binding region of carnosic acid with NDM-1 was not situated in the active region of protein. Due to binding to the allosteric pocket of carnosic acid, the active region conformation of NDM-1 was observed to have been altered. The distance from the active center of the NDM-1-CA complex was larger than that of the free protein, leading to loss of activity. Then, the mutation experiments showed that carnosic acid had lower inhibitory activity against mutated protein than wild-type proteins. Fluorescence experiments verified the results reported above. Thus, our data indicate that carnosic acid is a potential NDM-1 inhibitor and is a promising drug for the treatment of NDM-1 producing pathogens.
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Affiliation(s)
- Yanan Yang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Yan Guo
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Yonglin Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Xiyan Wang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Jianfeng Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun, China
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22
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Structure-based design of covalent inhibitors targeting metallo-β-lactamases. Eur J Med Chem 2020; 203:112573. [DOI: 10.1016/j.ejmech.2020.112573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 01/21/2023]
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23
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Chen C, Yang K. Ruthenium complexes as prospective inhibitors of metallo-β-lactamases to reverse carbapenem resistance. Dalton Trans 2020; 49:14099-14105. [PMID: 32996954 DOI: 10.1039/d0dt02430a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The widespread prevalence of metallo-β-lactamase (MβL)-mediated pathogens has seriously caused a loss of efficacy of carbapenem antibacterials, the last resort for the treatment of severe infectious diseases. The development of effective MβL inhibitors is an ideal alternative to restore the efficacy of carbapenems. Here we report that Ru complexes can irreversibly inhibit clinically relevant B1 subclass MβLs (NDM-1, IMP-1 and VIM-2) and potentiate meropenem efficacy against MβL-expressing bacteria in vitro and in a mice infection model. The Cys208 residue at the Zn(ii)-binding site and Met67 residue at the β-hairpin loop of an enzyme active pocket are critical for Ru complexes to inhibit NDM-1, which was verified by enzyme kinetics, thermodynamics, NDM-1-C208A mutation and MALDI-TOF-MS analysis. This study will undoubtedly aid efforts to develop metal-based MβL inhibitors in combination with carbapenems to deal with the clinical crisis of carbapenem-resistant E. coli harboring MβLs.
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Affiliation(s)
- 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.
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24
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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]
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25
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Chen J, Huang T, Gong X, Yu Z, Shi Y, Yan Y, Zheng Y, Liu X, Li G, Wu Y. Ruthenium‐Catalyzed
meta
‐Selective C−H Nitration of Biologically Important Aryltetrazoles. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jian Chen
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Tianle Huang
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Xinrui Gong
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Zhu‐Jun Yu
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Yuesen Shi
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Yu‐Hang Yan
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Yang Zheng
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Xuexin Liu
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Guo‐Bo Li
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
| | - Yong Wu
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of PharmacySichuan University Chengdu 610041 People's Republic of China
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26
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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.
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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
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27
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Yan Y, Li G, Li G. Principles and current strategies targeting metallo‐β‐lactamase mediated antibacterial resistance. Med Res Rev 2020; 40:1558-1592. [PMID: 32100311 DOI: 10.1002/med.21665] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 02/11/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Yu‐Hang Yan
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Gen Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Guo‐Bo Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
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28
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Yan YH, Chen J, Zhan Z, Yu ZJ, Li G, Guo L, Li GB, Wu Y, Zheng Y. Discovery of mercaptopropanamide-substituted aryl tetrazoles as new broad-spectrum metallo-β-lactamase inhibitors. RSC Adv 2020; 10:31377-31384. [PMID: 35520685 PMCID: PMC9056430 DOI: 10.1039/d0ra06405j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/14/2020] [Indexed: 12/01/2022] Open
Abstract
β-Lactam antibiotic resistance mediated by metallo-β-lactamases (MBL) has threatened global public health. There are currently no available inhibitors of MBLs for clinical use. We previously reported the ruthenium-catalyzed meta-selective C–H nitration synthesis method, leading to some meta-mercaptopropanamide substituted aryl tetrazoles as new potent MBL inhibitors. Here, we described the structure–activity relationship of meta- and ortho-mercaptopropanamide substituted aryl tetrazoles with clinically relevant MBLs. The resulting most potent compound 13a showed IC50 values of 0.044 μM, 0.396 μM and 0.71 μM against VIM-2, NDM-1 and IMP-1 MBL, respectively. Crystallographic analysis revealed that 13a chelated to active site zinc ions via the thiol group and interacted with the catalytically important residues Asn233 and Tyr67, providing further structural information for the development of thiol based MBL inhibitors. Compound 13a showed IC50 values of 0.044 μM, 0.396 μM and 0.71 μM against VIM-2, NDM-1 and IMP-1 MBL, respectively. It binds to chelates via active site zinc ions and forms interactions with residues on the L1 and L3 loops of VIM-2.![]()
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Affiliation(s)
- Yu-Hang Yan
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
| | - Jian Chen
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
| | - Zhen Zhan
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
| | - Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
| | - Gen Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
| | - Li Guo
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
| | - Yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
| | - Yongxiang Zheng
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- Sichuan Engineering Laboratory for Plant-Sourced Drug
- Sichuan Research Center for Drug Precision Industrial Technology
- West China School of Pharmacy
- Sichuan University
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29
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Discovery of [1,2,4]Triazole Derivatives as New Metallo-β-Lactamase Inhibitors. Molecules 2019; 25:molecules25010056. [PMID: 31877988 PMCID: PMC6982996 DOI: 10.3390/molecules25010056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 01/08/2023] Open
Abstract
The emergence and spread of metallo-β-lactamase (MBL)-mediated resistance to β-lactam antibacterials has already threatened the global public health. A clinically useful MBL inhibitor that can reverse β-lactam resistance has not been established yet. We here report a series of [1,2,4]triazole derivatives and analogs, which displayed inhibition to the clinically relevant subclass B1 (Verona integron-encoded MBL-2) VIM-2. 3-(4-Bromophenyl)-6,7-dihydro-5H-[1,2,4]triazolo [3,4-b][1,3]thiazine (5l) manifested the most potent inhibition with an IC50 (half-maximal inhibitory concentration) value of 38.36 μM. Investigations of 5l against other B1 MBLs and the serine β-lactamases (SBLs) revealed the selectivity to VIM-2. Molecular docking analyses suggested that 5l bound to the VIM-2 active site via the triazole involving zinc coordination and made hydrophobic interactions with the residues Phe61 and Tyr67 on the flexible L1 loop. This work provided new triazole-based MBL inhibitors and may aid efforts to develop new types of inhibitors combating MBL-mediated resistance.
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30
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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
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31
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The assemblage of covalent and metal binding dual functional scaffold for cross-class metallo-β-lactamases inhibition. Future Med Chem 2019; 11:2381-2394. [PMID: 31544522 DOI: 10.4155/fmc-2019-0008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: The discovery and development of novel broad-spectrum MβLs inhibitors are urgent to overcome antibiotic resistance mediated by MβLs. Methods & results: Herein, the synthesized 21 compounds exhibited potent inhibition to the clinically important MβLs (NDM-1, IMP-1 and ImiS) and effectively restored the antibacterial efficacy of cefazolin and imipenem against Escherichia coli harboring MβLs. 5b was first identified to be dual functional broad-spectrum MβLs inhibitor through assemblage of covalent and metal binding scaffold, which irreversibly inhibited B1, B2 MβLs via forming a Se–S covalent bond, and competitively inhibited B3 MβLs by coordinating the metals at active site. Conclusion: The designed compounds can serve as potent broad-spectrum MβLs inhibitors and combat MβLs-producing ‘superbug’ in combination with β-lactams.
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32
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Wang YL, Liu S, Yu ZJ, Lei Y, Huang MY, Yan YH, Ma Q, Zheng Y, Deng H, Sun Y, Wu C, Yu Y, Chen Q, Wang Z, Wu Y, Li GB. Structure-Based Development of (1-(3′-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-β-lactamases. J Med Chem 2019; 62:7160-7184. [PMID: 31269398 DOI: 10.1021/acs.jmedchem.9b00735] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yao-Ling Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Sha Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Zhu-Jun Yu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Yuan Lei
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Meng-Yi Huang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Qiang Ma
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Yang Zheng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Hui Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Ying Sun
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Chengyong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yamei Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Qiang Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Zhenling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yong Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
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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.
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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
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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
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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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.
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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
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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.
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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
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38
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Yu ZJ, Liu S, Zhou S, Li H, Yang F, Yang LL, Wu Y, Guo L, Li GB. Virtual target screening reveals rosmarinic acid and salvianolic acid A inhibiting metallo- and serine-β-lactamases. Bioorg Med Chem Lett 2018; 28:1037-1042. [PMID: 29477271 DOI: 10.1016/j.bmcl.2018.02.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 01/08/2023]
Abstract
Rosmarinic acid (RA), a polyphenolic phytochemical, has broad-spectrum biological and pharmacological activity. A virtual target screening method termed IFPTarget combined with enzyme inhibition assays led to the identification of the clinically relevant metallo-β-lactamase (MBL) VIM-2 as one of unexploited targets of RA. The enzyme kinetic studies indicated that RA is a fully reversible, substrate-competitive VIM-2 inhibitor. The isothermal titration calorimetry (ITC) analyses revealed that the initial binding of RA to VIM-2 is mainly due to enthalpy contribution. Further inhibition assays with RA related compounds revealed that salvianolic acid A, a derivative of RA, manifests potent inhibition to VIM-2, more interestingly, which shows inhibitory activity against the NDM-1, another clinically relevant MBL subtype, and the serine-β-lactamase TEM-1 that is structurally and mechanistically distinct from the VIM-2 and NDM-1.
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Affiliation(s)
- Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Sha Liu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Shu Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Hui Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Fan Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Ling-Ling Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Li Guo
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China.
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Zhang C, Pu YC, Yu ZJ, Wu CY, Brem J, McDonough MA, Schofield CJ, Li GB, Wu Y. Rh(iii)-Catalyzed directed C–H carbenoid coupling reveals aromatic bisphosphonates inhibiting metallo- and Serine-β-lactamases. Org Chem Front 2018. [DOI: 10.1039/c8qo00009c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–H coupling of arenes with diazo-methylene-diphosphonates enables efficient synthesis of new diphosphonates, which exhibit dual MBL and SBL inhibition.
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Affiliation(s)
- Chen Zhang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Yan-chi Pu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Cheng-yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Jürgen Brem
- Department of Chemistry
- University of Oxford
- Oxford
- UK
| | | | | | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
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