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Lee JH, Kim SG, Jang KM, Shin K, Jin H, Kim DW, Jeong BC, Lee SH. Elucidation of critical chemical moieties of metallo-β-lactamase inhibitors and prioritisation of target metallo-β-lactamases. J Enzyme Inhib Med Chem 2024; 39:2318830. [PMID: 38488135 PMCID: PMC10946278 DOI: 10.1080/14756366.2024.2318830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
The urgent demand for effective countermeasures against metallo-β-lactamases (MBLs) necessitates development of novel metallo-β-lactamase inhibitors (MBLIs). This study is dedicated to identifying critical chemical moieties within previously developed MBLIs, and critical MBLs should serve as the target in MBLI evaluations. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), a systematic literature analysis was conducted, and the NCBI RefSeq genome database was exploited to access the abundance profile and taxonomic distribution of MBLs and their variant types. Through the implementation of two distinct systematic approaches, we elucidated critical chemical moieties of MBLIs, providing pivotal information for rational drug design. We also prioritised MBLs and their variant types, highlighting the imperative need for comprehensive testing to ensure the potency and efficacy of the newly developed MBLIs. This approach contributes valuable information to advance the field of antimicrobial drug discovery.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang-Gyu Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
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Flori L, Brogi S, Sirous H, Calderone V. Disruption of Irisin Dimerization by FDA-Approved Drugs: A Computational Repurposing Approach for the Potential Treatment of Lipodystrophy Syndromes. Int J Mol Sci 2023; 24:ijms24087578. [PMID: 37108741 PMCID: PMC10145865 DOI: 10.3390/ijms24087578] [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: 03/22/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
In this paper, we present the development of a computer-based repurposing approach to identify FDA-approved drugs that are potentially able to interfere with irisin dimerization. It has been established that altered levels of irisin dimers are a pure hallmark of lipodystrophy (LD) syndromes. Accordingly, the identification of compounds capable of slowing down or precluding the irisin dimers' formation could represent a valuable therapeutic strategy in LD. Combining several computational techniques, we identified five FDA-approved drugs with satisfactory computational scores (iohexol, XP score = -7.70 kcal/mol, SP score = -5.5 kcal/mol, ΔGbind = -61.47 kcal/mol, ΔGbind (average) = -60.71 kcal/mol; paromomycin, XP score = -7.23 kcal/mol, SP score = -6.18 kcal/mol, ΔGbind = -50.14 kcal/mol, ΔGbind (average) = -49.13 kcal/mol; zoledronate, XP score = -6.33 kcal/mol, SP score = -5.53 kcal/mol, ΔGbind = -32.38 kcal/mol, ΔGbind (average) = -29.42 kcal/mol; setmelanotide, XP score = -6.10 kcal/mol, SP score = -7.24 kcal/mol, ΔGbind = -56.87 kcal/mol, ΔGbind (average) = -62.41 kcal/mol; and theophylline, XP score = -5.17 kcal/mol, SP score = -5.55 kcal/mol, ΔGbind = -33.25 kcal/mol, ΔGbind (average) = -35.29 kcal/mol) that are potentially able to disrupt the dimerization of irisin. For this reason, they deserve further investigation to characterize them as irisin disruptors. Remarkably, the identification of drugs targeting this process can offer novel therapeutic opportunities for the treatment of LD. Furthermore, the identified drugs could provide a starting point for a repositioning approach, synthesizing novel analogs with improved efficacy and selectivity against the irisin dimerization process.
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Affiliation(s)
- Lorenzo Flori
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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A fragment-based drug discovery strategy applied to the identification of NDM-1 β-lactamase inhibitors. Eur J Med Chem 2022; 240:114599. [PMID: 35841882 DOI: 10.1016/j.ejmech.2022.114599] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022]
Abstract
Hydrolysis of β-lactam drugs, a major class of antibiotics, by serine or metallo-β-lactamases (SBL or MBL) is one of the main mechanisms for antibiotic resistance. New Delhi Metallo-β-lactamase-1 (NDM-1), an acquired metallo-carbapenemase first reported in 2009, is currently considered one of the most clinically relevant targets for the development of β-lactam-β-lactamase inhibitor combinations active on NDM-producing clinical isolates. Identification of scaffolds that could be further rationally pharmacomodulated to design new and efficient NDM-1 inhibitors is thus urgently needed. Fragment-based drug discovery (FBDD) has become of great interest for the development of new drugs for the past few years and combination of several FBDD strategies, such as virtual and NMR screening, can reduce the drawbacks of each of them independently. Our methodology starting from a high throughput virtual screening on NDM-1 of a large library (more than 700,000 compounds) allowed, after slicing the hit molecules into fragments, to build a targeted library. These hit fragments were included in an in-house untargeted library fragments that was screened by Saturation Transfer Difference (STD) Nuclear Magnetic Resonance (NMR). 37 fragments were finally identified and used to establish a pharmacophore. 10 molecules based on these hit fragments were synthesized to validate our strategy. Indenone 89 that combined two identified fragments shows an inhibitory activity on NDM-1 with a Ki value of 4 μM.
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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Virtual screening identifies broad-spectrum β-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases. Sci Rep 2020; 10:12763. [PMID: 32728062 PMCID: PMC7391774 DOI: 10.1038/s41598-020-69431-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria are known to evade β-lactam antibiotic action by producing β-lactamases (BLs), including carbapenemases, which are able to hydrolyze nearly all available β-lactams. The production of BLs represents one of the best known and most targeted mechanisms of resistance in bacteria. We have performed the parallel screening of commercially available compounds against a panel of clinically relevant BLs: class A CTX-M-15 and KPC-2, subclass B1 NDM-1 and VIM-2 MBLs, and the class C P. aeruginosa AmpC. The results show that all BLs prefer scaffolds having electron pair donors: KPC-2 is preferentially inhibited by sulfonamide and tetrazole-based derivatives, NDM-1 by compounds bearing a thiol, a thiosemicarbazide or thiosemicarbazone moiety, while VIM-2 by triazole-containing molecules. Few broad-spectrum BLs inhibitors were identified; among these, compound 40 potentiates imipenem activity against an NDM-1-producing E. coli clinical strain. The binary complexes of the two most promising compounds binding NDM-1 and VIM-2 were obtained at high resolution, providing strong insights to improve molecular docking simulations, especially regarding the interaction of MBLs with inhibitors.
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Gavara L, Verdirosa F, Legru A, Mercuri PS, Nauton L, Sevaille L, Feller G, Berthomieu D, Sannio F, Marcoccia F, Tanfoni S, De Luca F, Gresh N, Galleni M, Docquier JD, Hernandez JF. 4-( N-Alkyl- and -Acyl-amino)-1,2,4-triazole-3-thione Analogs as Metallo-β-Lactamase Inhibitors: Impact of 4-Linker on Potency and Spectrum of Inhibition. Biomolecules 2020; 10:E1094. [PMID: 32717907 PMCID: PMC7465886 DOI: 10.3390/biom10081094] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 11/17/2022] Open
Abstract
To fight the increasingly worrying bacterial resistance to antibiotics, the discovery and development of new therapeutics is urgently needed. Here, we report on a new series of 1,2,4-triazole-3-thione compounds as inhibitors of metallo-β-lactamases (MBLs), which represent major resistance determinants to β-lactams, and especially carbapenems, in Gram-negative bacteria. These molecules are stable analogs of 4-amino-1,2,4-triazole-derived Schiff bases, where the hydrazone-like bond has been reduced (hydrazine series) or the 4-amino group has been acylated (hydrazide series); the synthesis and physicochemical properties thereof are described. The inhibitory potency was determined on the most clinically relevant acquired MBLs (IMP-, VIM-, and NDM-types subclass B1 MBLs). When compared with the previously reported hydrazone series, hydrazine but not hydrazide analogs showed similarly potent inhibitory activity on VIM-type enzymes, especially VIM-2 and VIM-4, with Ki values in the micromolar to submicromolar range. One of these showed broad-spectrum inhibition as it also significantly inhibited VIM-1 and NDM-1. Restoration of β-lactam activity in microbiological assays was observed for one selected compound. Finally, the binding to the VIM-2 active site was evaluated by isothermal titration calorimetry and a modeling study explored the effect of the linker structure on the mode of binding with this MBL.
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Affiliation(s)
- Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 34093 Montpellier, France; (A.L.); (L.S.)
| | - Federica Verdirosa
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Alice Legru
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 34093 Montpellier, France; (A.L.); (L.S.)
| | - Paola Sandra Mercuri
- Laboratoire des Macromolécules Biologiques, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, Institute of Chemistry B6 a, Sart-Tilman, 4000 Liège, Belgium; (P.S.M.); (M.G.)
| | - Lionel Nauton
- Institut de Chimie de Clermont-Ferrand, Université Clermont-Auvergne, CNRS, SIGMA Clermont, 63000 Clermont-Ferrand, France;
| | - Laurent Sevaille
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 34093 Montpellier, France; (A.L.); (L.S.)
| | - Georges Feller
- Laboratoire de Biochimie, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, B6, Sart-Tilman, 4000 Liège, Belgium;
| | - Dorothée Berthomieu
- Institut Charles Gerhardt, UMR5253, CNRS, Université de Montpellier, ENSCM, Cedex 5, 34296 Montpellier, France;
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Francesca Marcoccia
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Silvia Tanfoni
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Filomena De Luca
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR7616, Sorbonne Université, CNRS, 75252 Paris, France;
| | - Moreno Galleni
- Laboratoire des Macromolécules Biologiques, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, Institute of Chemistry B6 a, Sart-Tilman, 4000 Liège, Belgium; (P.S.M.); (M.G.)
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 34093 Montpellier, France; (A.L.); (L.S.)
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MBLinhibitors.com, a Website Resource Offering Information and Expertise for the Continued Development of Metallo--Lactamase Inhibitors. Biomolecules 2020; 10:biom10030459. [PMID: 32188106 PMCID: PMC7175331 DOI: 10.3390/biom10030459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 12/29/2022] Open
Abstract
In an effort to facilitate the discovery of new, improved inhibitors of the metallo-β-lactamases (MBLs), a new, interactive website called MBLinhibitors.com was developed. Despite considerable efforts from the science community, there are no clinical inhibitors of the MBLs, which are now produced by human pathogens. The website, MBLinhibitors.com, contains a searchable database of known MBL inhibitors, and inhibitors can be searched by chemical name, chemical formula, chemical structure, Simplified Molecular-Input Line-Entry System (SMILES) format, and by the MBL on which studies were conducted. The site will also highlight a “MBL Inhibitor of the Month”, and researchers are invited to submit compounds for this feature. Importantly, MBLinhibitors.com was designed to encourage collaboration, and researchers are invited to submit their new compounds, using the “Submit” function on the site, as well as their expertise using the “Collaboration” function. The intention is for this site to be interactive, and the site will be improved in the future as researchers use the site and suggest improvements. It is hoped that MBLinhibitors.com will serve as the one-stop site for any important information on MBL inhibitors and will aid in the discovery of a clinically useful MBL inhibitor.
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Saccoccia F, Brindisi M, Gimmelli R, Relitti N, Guidi A, Saraswati AP, Cavella C, Brogi S, Chemi G, Butini S, Papoff G, Senger J, Herp D, Jung M, Campiani G, Gemma S, Ruberti G. Screening and Phenotypical Characterization of Schistosoma mansoni Histone Deacetylase 8 ( SmHDAC8) Inhibitors as Multistage Antischistosomal Agents. ACS Infect Dis 2020; 6:100-113. [PMID: 31661956 DOI: 10.1021/acsinfecdis.9b00224] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Schistosomiasis (also known as bilharzia) is a neglected tropical disease caused by platyhelminths of the genus Schistosoma. The disease is endemic in tropical and subtropical areas of the world where water is infested by the intermediate parasite host, the snail. More than 800 million people live in endemic areas and more than 200 million are infected and require treatment. Praziquantel (PZQ) is the drug of choice for schistosomiasis treatment and transmission control being safe and very effective against adult worms of all the clinically relevant Schistosoma species. Unfortunately, it is ineffective on immature, juvenile worms; therefore, it does not prevent reinfection. Moreover, the risk of development and spread of drug resistance because of the widespread use of a single drug in such a large population represents a serious threat. Therefore, research aimed at identifying novel drugs to be used alone or in combination with PZQ are needed. Schistosoma mansoni histone deacetylase 8 (SmHDAC8) is a class I zinc-dependent HDAC, which is abundantly expressed in all stages of its life cycle, thus representing an interesting target for drug discovery. Through virtual screening and phenotypical characterization of selected hits, we discovered two main chemical classes of compounds characterized by the presence of a hydroxamate-based metal binding group coupled to a spiroindoline or a tricyclic thieno[3,2-b]indole core as capping groups. Some of the compounds of both classes were deeply investigated and showed to impair viability of larval, juvenile, and adult schistosomes, to impact egg production in vitro and/or to induce morphological alterations of the adult schistosome reproductive systems. Noteworthy, all of them inhibit the recombinant form of SmHDAC8 enzyme in vitro. Overall, we identified very interesting scaffolds, paving the way to the development of effective antischistosomal agents.
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Affiliation(s)
- Fulvio Saccoccia
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Margherita Brindisi
- Department of Excellence of Pharmacy, University of Napoli Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Roberto Gimmelli
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Nicola Relitti
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Alessandra Guidi
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - A Prasanth Saraswati
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Caterina Cavella
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Simone Brogi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Giulia Chemi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Stefania Butini
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Giuliana Papoff
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Johanna Senger
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Daniel Herp
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Giuseppe Campiani
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Sandra Gemma
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Giovina Ruberti
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
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Sirous H, Chemi G, Campiani G, Brogi S. An integrated in silico screening strategy for identifying promising disruptors of p53-MDM2 interaction. Comput Biol Chem 2019; 83:107105. [DOI: 10.1016/j.compbiolchem.2019.107105] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 10/26/2022]
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A Repurposing Approach for Uncovering the Anti-Tubercular Activity of FDA-Approved Drugs with Potential Multi-Targeting Profiles. Molecules 2019; 24:molecules24234373. [PMID: 31795400 PMCID: PMC6930672 DOI: 10.3390/molecules24234373] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) is one of the top 10 causes of death worldwide. This scenario is further complicated by the insurgence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. The identification of appropriate drugs with multi-target affinity profiles is considered to be a widely accepted strategy to overcome the rapid development of resistance. The aim of this study was to discover Food and Drug Administration (FDA)-approved drugs possessing antimycobacterial activity, potentially coupled to an effective multi-target profile. An integrated screening platform was implemented based on computational procedures (high-throughput docking techniques on the target enzymes peptide deformylase and Zmp1) and in vitro phenotypic screening assays using two models to evaluate the activity of the selected drugs against Mycobacterium tuberculosis (Mtb), namely, growth of Mtb H37Rv and of two clinical isolates in axenic media, and infection of peripheral blood mononuclear cells with Mtb. Starting from over 3000 FDA-approved drugs, we selected 29 marketed drugs for submission to biological evaluation. Out of 29 drugs selected, 20 showed antimycobacterial activity. Further characterization suggested that five drugs possessed promising profiles for further studies. Following a repurposing strategy, by combining computational and biological efforts, we identified marketed drugs with relevant antimycobacterial profiles.
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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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Computational Approaches for Drug Discovery. Molecules 2019; 24:molecules24173061. [PMID: 31443558 PMCID: PMC6749237 DOI: 10.3390/molecules24173061] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
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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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14
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Kaushik A, Kaushik M, Lather V, Dua J. Recent Review on Subclass B1 Metallo-β-lactamases Inhibitors: Sword for Antimicrobial Resistance. Curr Drug Targets 2019; 20:756-762. [DOI: 10.2174/1389450120666181217101812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/03/2018] [Accepted: 12/11/2018] [Indexed: 01/17/2023]
Abstract
An emerging crisis of antibiotic resistance for microbial pathogens is alarming all the nations,
posing a global threat to human health. The production of the metallo-β-lactamase enzyme is the
most powerful strategy of bacteria to produce resistance. An efficient way to combat this global health
threat is the development of broad/non-specific type of metallo-β-lactamase inhibitors, which can inhibit
the different isoforms of the enzyme. Till date, there are no clinically active drugs against metallo-
β-lactamase. The lack of efficient drug molecules against MBLs carrying bacteria requires continuous
research efforts to overcome the problem of multidrug-resistance bacteria. The present review will
discuss the clinically potent molecules against different variants of B1 metallo-β-lactamase.
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Affiliation(s)
| | | | - Viney Lather
- Amity institute of Pharmacy, Amity University, Noida, India
| | - J.S. Dua
- School of Pharmacy, MMU, Sadopur, Ambala, India
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15
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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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16
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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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17
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Docquier JD, Mangani S. An update on β-lactamase inhibitor discovery and development. Drug Resist Updat 2017; 36:13-29. [PMID: 29499835 DOI: 10.1016/j.drup.2017.11.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 11/27/2022]
Abstract
Antibiotic resistance, and the emergence of pan-resistant clinical isolates, seriously threatens our capability to treat bacterial diseases, including potentially deadly hospital-acquired infections. This growing issue certainly requires multiple adequate responses, including the improvement of both diagnosis methods and use of antibacterial agents, and obviously the development of novel antibacterial drugs, especially active against Gram-negative pathogens, which represent an urgent medical need. Considering the clinical relevance of both β-lactam antibiotics and β-lactamase-mediated resistance, the discovery and development of combinations including a β-lactamase inhibitor seems to be particularly attractive, despite being extremely challenging due to the enormous diversity, both structurally and mechanistically, of the potential β-lactamase targets. This review will cover the evolution of currently available β-lactamase inhibitors along with the most recent research leading to new β-lactamase inhibitors of potential clinical interest or already in the stage of clinical development.
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Affiliation(s)
- Jean-Denis Docquier
- Department of Medical Biotechnology, University of Siena, Viale Bracci 16, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
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18
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Sevaille L, Gavara L, Bebrone C, De Luca F, Nauton L, Achard M, Mercuri P, Tanfoni S, Borgianni L, Guyon C, Lonjon P, Turan-Zitouni G, Dzieciolowski J, Becker K, Bénard L, Condon C, Maillard L, Martinez J, Frère JM, Dideberg O, Galleni M, Docquier JD, Hernandez JF. 1,2,4-Triazole-3-thione Compounds as Inhibitors of Dizinc Metallo-β-lactamases. ChemMedChem 2017; 12:972-985. [DOI: 10.1002/cmdc.201700186] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/12/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Laurent Sevaille
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Carine Bebrone
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
- Present address: Symbiose Biomaterials S.A., GIGA Bât. B34; 1 avenue de l'Hôpital 4000 Liège Belgium
| | - Filomena De Luca
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Lionel Nauton
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR5075 CNRS, CEA; Université Joseph Fourier; 41 rue Jules Horowitz 38027 Grenoble cedex 1 France
- Present address: Institut de Chimie de Clermont-Ferrand, UMR6296 CNRS; Université Clermont Auvergne; 63000 Clermont-Ferrand France
| | - Maud Achard
- EMBL Outstation c/o DESY; Notkestrasse 85 22603 Hamburg Germany
- Present address: School of Chemistry and Molecular Bioscience; University of Queensland, St. Lucia; Brisbane QLD 4072 Australia
| | - Paola Mercuri
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Silvia Tanfoni
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Luisa Borgianni
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Carole Guyon
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Pauline Lonjon
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
- Present address: CERN, HSE/SEE/SI; 1211 Geneva 23 Switzerland
| | - Gülhan Turan-Zitouni
- Department of Pharmaceutical Chemistry; Anadolu University, Faculty of Pharmacy; 26470 Eskisehir Turkey
| | - Julia Dzieciolowski
- Chair of Biochemistry and Molecular Biology, Interdisciplinary Research Center; Justus Liebig University; Heinrich-Buff-Ring 26-32 35392 Giessen Germany
| | - Katja Becker
- Chair of Biochemistry and Molecular Biology, Interdisciplinary Research Center; Justus Liebig University; Heinrich-Buff-Ring 26-32 35392 Giessen Germany
| | - Lionel Bénard
- UMR8226, CNRS, Université Pierre et Marie Curie; Institut de Biologie Physico-Chimique; 13 rue Pierre et Marie Curie 75005 Paris France
| | - Ciaran Condon
- UMR8261, CNRS, Université Paris-Diderot; Institut de Biologie Physico-Chimique; 13 rue Pierre et Marie Curie 75005 Paris France
| | - Ludovic Maillard
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Jean-Marie Frère
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Otto Dideberg
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR5075 CNRS, CEA; Université Joseph Fourier; 41 rue Jules Horowitz 38027 Grenoble cedex 1 France
| | - Moreno Galleni
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
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