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Ortega-Balleza JL, Vázquez-Jiménez LK, Ortiz-Pérez E, Avalos-Navarro G, Paz-González AD, Lara-Ramírez EE, Rivera G. Current Strategy for Targeting Metallo-β-Lactamase with Metal-Ion-Binding Inhibitors. Molecules 2024; 29:3944. [PMID: 39203022 PMCID: PMC11356879 DOI: 10.3390/molecules29163944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Currently, antimicrobial resistance (AMR) is a serious health problem in the world, mainly because of the rapid spread of multidrug-resistant (MDR) bacteria. These include bacteria that produce β-lactamases, which confer resistance to β-lactams, the antibiotics with the most prescriptions in the world. Carbapenems are particularly noteworthy because they are considered the ultimate therapeutic option for MDR bacteria. However, this group of antibiotics can also be hydrolyzed by β-lactamases, including metallo-β-lactamases (MBLs), which have one or two zinc ions (Zn2+) on the active site and are resistant to common inhibitors of serine β-lactamases, such as clavulanic acid, sulbactam, tazobactam, and avibactam. Therefore, the design of inhibitors against MBLs has been directed toward various compounds, with groups such as nitrogen, thiols, and metal-binding carboxylates, or compounds such as bicyclic boronates that mimic hydrolysis intermediates. Other compounds, such as dipicolinic acid and aspergillomarasmin A, have also been shown to inhibit MBLs by chelating Zn2+. In fact, recent inhibitors are based on Zn2+ chelation, which is an important factor in the mechanism of action of most MBL inhibitors. Therefore, in this review, we analyzed the current strategies for the design and mechanism of action of metal-ion-binding inhibitors that combat MDR bacteria.
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Affiliation(s)
- Jessica L. Ortega-Balleza
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (J.L.O.-B.); (L.K.V.-J.); (E.O.-P.); (A.D.P.-G.); (E.E.L.-R.)
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Ciudad de México 03940, Mexico
| | - Lenci K. Vázquez-Jiménez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (J.L.O.-B.); (L.K.V.-J.); (E.O.-P.); (A.D.P.-G.); (E.E.L.-R.)
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Ciudad de México 03940, Mexico
| | - Eyra Ortiz-Pérez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (J.L.O.-B.); (L.K.V.-J.); (E.O.-P.); (A.D.P.-G.); (E.E.L.-R.)
| | - Guadalupe Avalos-Navarro
- Departamento de Ciencias Médicas y de la Vida, Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán 47810, Mexico;
| | - Alma D. Paz-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (J.L.O.-B.); (L.K.V.-J.); (E.O.-P.); (A.D.P.-G.); (E.E.L.-R.)
| | - Edgar E. Lara-Ramírez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (J.L.O.-B.); (L.K.V.-J.); (E.O.-P.); (A.D.P.-G.); (E.E.L.-R.)
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (J.L.O.-B.); (L.K.V.-J.); (E.O.-P.); (A.D.P.-G.); (E.E.L.-R.)
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Na TU, Sander V, Davidson AJ, Lin R, Hermant YO, Hardie Boys MT, Pletzer D, Campbell G, Ferguson SA, Cook GM, Allison JR, Brimble MA, Northrop BH, Cameron AJ. Allenamides as a Powerful Tool to Incorporate Diversity: Thia-Michael Lipidation of Semisynthetic Peptides and Access to β-Keto Amides. Angew Chem Int Ed Engl 2024:e202407764. [PMID: 38932510 DOI: 10.1002/anie.202407764] [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: 04/24/2024] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
Lipopeptides are an important class of biomolecules for drug development. Compared with conventional acylation, a chemoselective lipidation strategy offers a more efficient strategy for late-stage structural derivatisation of a peptide scaffold. It provides access to chemically diverse compounds possessing intriguing and non-native moieties. Utilising an allenamide, we report the first semisynthesis of antimicrobial lipopeptides leveraging a highly efficient thia-Michael addition of chemically diverse lipophilic thiols. Using chemoenzymatically prepared polymyxin B nonapeptide (PMBN) as a model scaffold, an optimised allenamide-mediated thia-Michael addition effected rapid and near quantitative lipidation, affording vinyl sulfide-linked lipopeptide derivatives. Harnessing the utility of this new methodology, 22 lipophilic thiols of unprecedented chemical diversity were introduced to the PMBN framework. These included alkyl thiols, substituted aromatic thiols, heterocyclic thiols and those bearing additional functional groups (e.g., amines), ultimately yielding analogues with potent Gram-negative antimicrobial activity and substantially attenuated nephrotoxicity. Furthermore, we report facile routes to transform the allenamide into a β-keto amide on unprotected peptides, offering a powerful "jack-of-all-trades" synthetic intermediate to enable further peptide modification.
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Affiliation(s)
- Tae-Ung Na
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
| | - Veronika Sander
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- Department of Molecular Medicine and Pathology, The University of Auckland, 85 Park Road, Auckland, 1023, New Zealand
| | - Alan J Davidson
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- Department of Molecular Medicine and Pathology, The University of Auckland, 85 Park Road, Auckland, 1023, New Zealand
| | - Rolland Lin
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
| | - Yann O Hermant
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
| | - Madeleine T Hardie Boys
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- Department of Microbiology and Immunology, School of Medical Sciences, The University of Otago, 720 Cumberland Street, Dunedin, 9054, New Zealand
| | - Daniel Pletzer
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- Department of Microbiology and Immunology, School of Medical Sciences, The University of Otago, 720 Cumberland Street, Dunedin, 9054, New Zealand
| | - Georgia Campbell
- Department of Microbiology and Immunology, School of Medical Sciences, The University of Otago, 720 Cumberland Street, Dunedin, 9054, New Zealand
| | - Scott A Ferguson
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- Department of Microbiology and Immunology, School of Medical Sciences, The University of Otago, 720 Cumberland Street, Dunedin, 9054, New Zealand
| | - Gregory M Cook
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- Department of Microbiology and Immunology, School of Medical Sciences, The University of Otago, 720 Cumberland Street, Dunedin, 9054, New Zealand
| | - Jane R Allison
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
| | - Brian H Northrop
- Department of Chemistry, Wesleyan University, 52 Lawn Ave., Middletown, CT 06459, U.S.A
| | - Alan J Cameron
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
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Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, Kazlauskas E. Recent advances in computational and experimental protein-ligand affinity determination techniques. Expert Opin Drug Discov 2024; 19:649-670. [PMID: 38715415 DOI: 10.1080/17460441.2024.2349169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved. AREAS COVERED In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design. EXPERT OPINION The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.
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Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Hwang TL, Lin JY, Kuo LM, Kumar Dhandabani G, Hsieh PW. Design and synthesis of sirtinol analogs as human neutrophil elastase inhibitors. Bioorg Med Chem Lett 2024; 97:129544. [PMID: 37939864 DOI: 10.1016/j.bmcl.2023.129544] [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: 07/21/2023] [Revised: 09/22/2023] [Accepted: 11/04/2023] [Indexed: 11/10/2023]
Abstract
Human neutrophil elastase (HNE) overexpression has a crucial role in most acute inflammation and alpha1-antitrypsin deficiency syndromes observed in humans, triggering neutrophil invasion and activation of macrophage inflammatory and proteolytic effects, leading to tissue damage. Manipulating HNE level homeostasis could potentially help treat neutrophilic inflammation. Previous studies have shown that sirtinol (1) has a specific influence on HNE and potently attenuates acute lung injury and hepatic injury mediated by lipopolysaccharide or trauma hemorrhage. Therefore, 1 was chosen as the model structure to obtain more potent anti-HNE agents. In the present study, we synthesized a series of sirtinol analogues and determined their inhibitory effects on HNE. Structure-activity relationship (SAR) studies showed that swapping the imine and methyl groups of the sirtinol scaffold with diazene and carboxyl groups, respectively, enhances the HNE inhibiting potency. Compound 29 exhibited the highest potency in the SAR study and showed dual inhibitory effects on HNE and proteinase 3 with IC50 values of 4.91 and 20.69 µM, respectively. Furthermore, 29 was confirmed to have dual impacts on inhibiting O2•- generation and elastase release in cell-based assays with IC50 values of 0.90 and 1.86 µM, respectively. These findings suggest that 29 is a promising candidate for developing HNE inhibitors in the treatment of neutrophilic inflammatory diseases.
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Affiliation(s)
- Tsong-Long Hwang
- Graduate Institute of Natural Products, School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Anesthesiology, Chang Gung Memorial Hospital, Linkou, Taiwan; Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan; Chinese Herbal Medicine Research Team, Healthy Aging Research Center, Chang Gung University, Taoyuan, Taiwan.
| | - Jing-Yi Lin
- Graduate Institute of Natural Products, School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Liang-Mou Kuo
- Department of General Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan.
| | - Ganesh Kumar Dhandabani
- Graduate Institute of Natural Products, School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Pei-Wen Hsieh
- Graduate Institute of Natural Products, School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan; Department of General Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan.
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Caburet J, Verdirosa F, Moretti M, Roulier B, Simoncelli G, Haudecoeur R, Ghazi S, Jamet H, Docquier JD, Boucherle B, Peuchmaur M. Aurones and derivatives as promising New Delhi metallo-β-lactamase (NDM-1) inhibitors. Bioorg Med Chem 2024; 97:117559. [PMID: 38109811 DOI: 10.1016/j.bmc.2023.117559] [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: 07/10/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Bacterial resistance is undoubtedly one of the main public health concerns especially with the emergence of metallo-β-lactamases (MBLs) able to hydrolytically inactivate β-lactam antibiotics. Currently, there are no inhibitors of MBLs in clinical use to rescue antibiotic action and the New Delhi metallo-β-lactamase-1 (NDM-1) is still considered as one of the most relevant targets for inhibitor development. Following a fragment-based strategy to find new NDM-1 inhibitors, we identified aurone as a promising scaffold. A series of 60 derivatives were then evaluated and two of them were identified as promising inhibitors with Ki values as low as 1.7 and 2.5 µM. Moreover, these two most active compounds were able to potentiate meropenem in in vitro antimicrobial susceptibility assays. The molecular modelling provided insights about their likely interactions with the active site of NDM-1, thus enabling further improvement in the structure of this new inhibitor family.
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Affiliation(s)
| | - Federica Verdirosa
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | - Matis Moretti
- Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | | | - Giorgia Simoncelli
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | | | - Somayeh Ghazi
- Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Hélène Jamet
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy; Laboratoire de Bactériologie Moléculaire, UR-InBioS, Université de Liège, 4000 Liège, Belgium
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