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Xiao H, Li J, Yang D, Du J, Li J, Lin S, Zhou H, Sun P, Xu J. Multidimensional Criteria for Virtual Screening of PqsR Inhibitors Based on Pharmacophore, Docking, and Molecular Dynamics. Int J Mol Sci 2024; 25:1869. [PMID: 38339148 PMCID: PMC10856439 DOI: 10.3390/ijms25031869] [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: 12/13/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Pseudomonas aeruginosa is a clinically challenging pathogen due to its high resistance to antibiotics. Quorum sensing inhibitors (QSIs) have been proposed as a promising strategy to overcome this resistance by interfering with the bacterial communication system. Among the potential targets of QSIs, PqsR is a key regulator of quorum sensing in Pseudomonas aeruginosa. However, the current research on PqsR inhibitors is limited by the lack of diversity in the chemical structures and the screening methods. Therefore, this study aims to develop a multidimensional screening model for PqsR inhibitors based on both ligand- and receptor-based approaches. First, a pharmacophore model was constructed from a training set of PqsR inhibitors to identify the essential features and spatial arrangement for the activity. Then, molecular docking and dynamics simulations were performed to explore the core interactions between PqsR inhibitors and their receptor. The results indicate that an effective PqsR inhibitor should possess two aromatic rings, one hydrogen bond acceptor, and two hydrophobic groups and should form strong interactions with the following four amino acid residues: TYR_258, ILE_236, LEU_208, and GLN_194. Moreover, the docking score and the binding free energy should be lower than -8 kcal/mol and -40 kcal/mol, respectively. Finally, the validity of the multidimensional screening model was confirmed by a test set of PqsR inhibitors, which showed a higher accuracy than the existing screening methods based on single characteristics. This multidimensional screening model would be a useful tool for the discovery and optimization of PqsR inhibitors in the future.
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Affiliation(s)
- Haichuan Xiao
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
| | - Jiahao Li
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
| | - Dongdong Yang
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
| | - Jiarui Du
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
| | - Jie Li
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
| | - Shuqi Lin
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
| | - Haibo Zhou
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
| | - Pinghua Sun
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, School of Pharmacy, Shihezi University, Shihezi 832003, China
| | - Jun Xu
- College of Pharmacy, Jinan University, Guangzhou 510632, China; (H.X.); (J.L.); (D.Y.); (J.D.); (J.L.); (S.L.); (H.Z.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
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Hamed MM, Abdelsamie AS, Rox K, Schütz C, Kany AM, Röhrig T, Schmelz S, Blankenfeldt W, Arce‐Rodriguez A, Borrero‐de Acuña JM, Jahn D, Rademacher J, Ringshausen FC, Cramer N, Tümmler B, Hirsch AKH, Hartmann RW, Empting M. Towards Translation of PqsR Inverse Agonists: From In Vitro Efficacy Optimization to In Vivo Proof-of-Principle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204443. [PMID: 36596691 PMCID: PMC9929129 DOI: 10.1002/advs.202204443] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Pseudomonas aeruginosa (PA) is an opportunistic human pathogen, which is involved in a wide range of dangerous infections. It develops alarming resistances toward antibiotic treatment. Therefore, alternative strategies, which suppress pathogenicity or synergize with antibiotic treatments are in great need to combat these infections more effectively. One promising approach is to disarm the bacteria by interfering with their quorum sensing (QS) system, which regulates the release of various virulence factors as well as biofilm formation. Herein, this work reports the rational design, optimization, and in-depth profiling of a new class of Pseudomonas quinolone signaling receptor (PqsR) inverse agonists. The resulting frontrunner compound features a pyrimidine-based scaffold, high in vitro and in vivo efficacy, favorable pharmacokinetics as well as clean safety pharmacology characteristics, which provide the basis for potential pulmonary as well as systemic routes of administration. An X-ray crystal structure in complex with PqsR facilitated further structure-guided lead optimization. The compound demonstrates potent pyocyanin suppression, synergizes with aminoglycoside antibiotic tobramycin against PA biofilms, and is active against a panel of clinical isolates from bronchiectasis patients. Importantly, this in vitro effect translated into in vivo efficacy in a neutropenic thigh infection model in mice providing a proof-of-principle for adjunctive treatment scenarios.
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Affiliation(s)
- Mostafa M. Hamed
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Ahmed S. Abdelsamie
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of Chemistry of Natural and Microbial ProductsInstitute of Pharmaceutical and Drug Industries ResearchNational Research CentreEl‐Buhouth St.DokkiCairo12622Egypt
| | - Katharina Rox
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of Chemical Biology (CBIO)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
| | - Christian Schütz
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Andreas M. Kany
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Teresa Röhrig
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Stefan Schmelz
- Department of Structure and Function of Proteins (SFPR)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
| | - Wulf Blankenfeldt
- Department of Structure and Function of Proteins (SFPR)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
- Institute for BiochemistryBiotechnology and BioinformaticsTechnische Universität BraunschweigBraunschweigGermany
| | | | - José Manuel Borrero‐de Acuña
- Institute of MicrobiologyTechnische Universität Braunschweig38106BraunschweigGermany
- Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig38106BraunschweigGermany
- Departamento de MicrobiologíaFacultad de BiologíaUniversidad de SevillaAv. de la Reina Mercedesno. 6SevillaCP 41012Spain
| | - Dieter Jahn
- Institute of MicrobiologyTechnische Universität Braunschweig38106BraunschweigGermany
- Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig38106BraunschweigGermany
| | - Jessica Rademacher
- Department for Respiratory MedicineMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
| | - Felix C. Ringshausen
- Department for Respiratory MedicineMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
- European Reference Network on Rare and Complex Respiratory Diseases (ERN‐ LUNG)FrankfurtGermany
| | - Nina Cramer
- Department for Pediatric PneumologyAllergology and NeonatologyMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
| | - Burkhard Tümmler
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
- Department for Pediatric PneumologyAllergology and NeonatologyMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
| | - Anna K. H. Hirsch
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
| | - Rolf W. Hartmann
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
| | - Martin Empting
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
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Zhang B, Yang Y, Xie W, He W, Xie J, Liu W. Identifying Algicides of Enterobacter hormaechei F2 for Control of the Harmful Alga Microcystis aeruginosa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19137556. [PMID: 35805215 PMCID: PMC9265343 DOI: 10.3390/ijerph19137556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 01/27/2023]
Abstract
Eutrophication has become an increasingly serious environmental issue and has contributed towards an explosion in harmful algal blooms (HABs) affecting local development. HABs can cause serious threats to ecosystems and human health. A newly isolated algicidal strain, Enterobacter hormaechei F2, showed high algicidal activity against the typical HAB species Microcystis aeruginosa. Potential algicides were detected through liquid chromatograph–mass spectrometer analysis, revealing that prodigiosin is an algicide and PQS is a quorum sensing molecule. RNA-seq was used to understand the algicidal mechanisms and the related pathways. We concluded that the metabolism of prodigiosin and PQS are active at the transcriptional level. The findings indicate that E. hormaechei F2 can be used as a potential biological agent to control harmful algal blooms to prevent the deterioration of the ecological and economic value of water bodies.
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Affiliation(s)
- Bin Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (B.Z.); (W.X.); (W.H.); (J.X.)
| | - Ying Yang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China;
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Wenjia Xie
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (B.Z.); (W.X.); (W.H.); (J.X.)
| | - Wei He
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (B.Z.); (W.X.); (W.H.); (J.X.)
| | - Jia Xie
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (B.Z.); (W.X.); (W.H.); (J.X.)
| | - Wei Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (B.Z.); (W.X.); (W.H.); (J.X.)
- Guangdong Provincial Key Laboratory of Environmental Pollution and Remediation Technology, Guangzhou 510006, China
- Correspondence:
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Drug Repurposing Targeting Pseudomonas aeruginosa MvfR Using Docking, Virtual Screening, Molecular Dynamics, and Free-Energy Calculations. Antibiotics (Basel) 2022; 11:antibiotics11020185. [PMID: 35203788 PMCID: PMC8868191 DOI: 10.3390/antibiotics11020185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative bacterium responsible for acute and chronic infections in planktonic state or in biofilms. The sessile structures are known to confer physical stability, increase virulence, and work as a protective armor against antimicrobial compounds. P. aeruginosa can control the expression of genes, population density, and biofilm formation through a process called quorum sensing (QS), a rather complex and hierarchical system of communication. A recent strategy to try and overcome bacterial resistance is to target QS proteins. In this study, a combined multi-level computational approach was applied to find possible inhibitors against P. aeruginosa QS regulator protein MvfR, also known as PqsR, using a database of approved FDA drugs, as a repurposing strategy. Fifteen compounds were identified as highly promising putative MvfR inhibitors. On those 15 MvfR ligand complexes, molecular dynamic simulations and MM/GBSA free-energy calculations were performed to confirm the docking predictions and elucidate on the mode of interaction. Ultimately, the five compounds that presented better binding free energies of association than the reference molecules (a known antagonist, M64 and a natural inducer, 2-nonyl-4-hydroxyquinoline) were highlighted as very promising MvfR inhibitors.
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Liu J, Hou JS, Chang YQ, Peng LJ, Zhang XY, Miao ZY, Sun PH, Lin J, Chen WM. New Pqs Quorum Sensing System Inhibitor as an Antibacterial Synergist against Multidrug-Resistant Pseudomonas aeruginosa. J Med Chem 2021; 65:688-709. [PMID: 34951310 DOI: 10.1021/acs.jmedchem.1c01781] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Development of new bacterial biofilm inhibitors as antibacterial synergists is an effective strategy to solve the resistance of Pseudomonas aeruginosa. In this paper, a series of 3-hydroxy-pyridin-4(1H)-ones were synthesized and evaluated, and the hit compound (20p) was identified with the effects of inhibiting the production of pyocyanin (IC50 = 8.6 μM) and biofilm formation (IC50 = 4.5 μM). Mechanistic studies confirmed that 20p inhibits the formation of bacterial biofilm by inhibiting the expression of pqsA, blocking pqs quorum sensing system quinolone biosynthesis. Moreover, we systematically investigated the bactericidal effects of combining currently approved antibiotics for CF including tobramycin, ciprofloxacin, and colistin E with 20p, which showed obvious antibacterial synergy to overcome antibiotics resistance in multidrug-resistant P. aeruginosa biofilms. The result indicates that compound 20p may be used in the future as a potentially novel antibacterial synergist candidate for the treatment of P. aeruginosa infections.
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Affiliation(s)
- Jun Liu
- College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Jin-Song Hou
- College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Yi-Qun Chang
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Li-Jun Peng
- College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Xiao-Yi Zhang
- College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Zhi-Ying Miao
- College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Ping-Hua Sun
- College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Jing Lin
- College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Wei-Min Chen
- College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
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Duplantier M, Lohou E, Sonnet P. Quorum Sensing Inhibitors to Quench P. aeruginosa Pathogenicity. Pharmaceuticals (Basel) 2021; 14:1262. [PMID: 34959667 PMCID: PMC8707152 DOI: 10.3390/ph14121262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/22/2022] Open
Abstract
The emergence and the dissemination of multidrug-resistant bacteria constitute a major public health issue. Among incriminated Gram-negative bacteria, Pseudomonas aeruginosa has been designated by the WHO as a critical priority threat. During the infection process, this pathogen secretes various virulence factors in order to adhere and colonize host tissues. Furthermore, P. aeruginosa has the capacity to establish biofilms that reinforce its virulence and intrinsic drug resistance. The regulation of biofilm and virulence factor production of this micro-organism is controlled by a specific bacterial communication system named Quorum Sensing (QS). The development of anti-virulence agents targeting QS that could attenuate P. aeruginosa pathogenicity without affecting its growth seems to be a promising new therapeutic strategy. This could prevent the selective pressure put on bacteria by the conventional antibiotics that cause their death and promote resistant strain survival. This review describes the QS-controlled pathogenicity of P. aeruginosa and its different specific QS molecular pathways, as well as the recent advances in the development of innovative QS-quenching anti-virulence agents to fight anti-bioresistance.
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Affiliation(s)
| | | | - Pascal Sonnet
- AGIR, UR4294, UFR of Pharmacy, Jules Verne University of Picardie, 80037 Amiens, France; (M.D.); (E.L.)
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7
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Zhao WW, Shao YC, Wang AN, Huang JL, He CY, Cui BD, Wan NW, Chen YZ, Han WY. Diazotrifluoroethyl Radical: A CF 3-Containing Building Block in [3 + 2] Cycloaddition. Org Lett 2021; 23:9256-9261. [PMID: 34802247 DOI: 10.1021/acs.orglett.1c03603] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We present herein a visible-light-induced [3 + 2] cycloaddition of a hypervalent iodine(III) reagent with α-ketoacids for the construction of 5-CF3-1,3,4-oxadiazoles that are of importance in medicinal chemistry. The reaction proceeds smoothly without a photocatalyst, metal, or additive under mild conditions. Different from the well-established trifluorodiazoethane (CF3CHN2), the diazotrifluoroethyl radical [CF3C(·)N2], a trifluoroethylcarbyne (CF3CĊ:) equivalent and an unusual CF3-containing building block, is involved in the present reaction system.
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Affiliation(s)
- Wen-Wen Zhao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China
| | - Yong-Chao Shao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China
| | - An-Ni Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China
| | - Jia-Li Huang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China
| | - Chun-Yang He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, P. R. China
| | - Bao-Dong Cui
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, P. R. China
| | - Nan-Wei Wan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, P. R. China
| | - Yong-Zheng Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, P. R. China
| | - Wen-Yong Han
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, P. R. China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, P. R. China
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8
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 37118182 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 352] [Impact Index Per Article: 117.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations. ![]()
Antimicrobial resistance is an increasing threat to public health and encouraging the development of new antimicrobials is one of the most important ways to address the problem. This Roadmap article aims to bring together industrial, academic and political partners, and proposes both short-term and long-term solutions to this challenge.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J V Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
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9
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Pham EC, Truong TN, Dong NH, Vo DD, Hong Do TT. Synthesis of a Series of Novel 2-Amino-5-Substituted 1,3,4-oxadiazole and 1,3,4-thiadiazole Derivatives as Potential Anticancer, Antifungal and Antibacterial Agents. Med Chem 2021; 18:558-573. [PMID: 34344293 DOI: 10.2174/1573406417666210803170637] [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: 11/14/2020] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Many compounds containing a five-membered heterocyclic ring display exceptional chemical properties and versatile biological activities. OBJECTIVE The objective of the present study was the desire to prepare the 5-substituted 2-amino-1,3,4-oxadiazole and 2-amino-1,3,4-thiadiazole derivatives and evaluate their potential anticancer, antibacterial and antifungal activities. METHODS Twenty-seven derivatives were synthesized by iodine-mediated cyclization of semicarbazones or thiosemicarbazones obtained from condensation of semicarbazide or thiosemicarbazide and aldehydes. The structures were confirmed by 1H-NMR, 13C-NMR and MS spectra. The antibacterial and antifungal activities were evaluated by diffusion method and the anticancer activities were evaluated by MTT assay. RESULTS Twenty-seven derivatives have been synthesized in moderate to good yields. A number of derivatives exhibited potential antibacterial, antifungal and anticancer activities. CONCLUSION Compounds (1b, 1e and 1g) showed antibacterial activity against Streptococcus faecalis, MSSA and MRSA with MIC ranging between 4 to 64 µg/mL. Compound (2g) showed antifungal activity against Candida albicans (8 µg/mL) and Aspergillus niger (64 µg/mL). Compound (1o) exhibited high cytotoxic activity against HepG2 cell line (IC50 value 8.6 µM), which is comparable to the activity of paclitaxel, and is non-toxic on LLC-PK1 normal cell line. The structure activity relationship and molecular docking study of the synthesized compounds are also reported.
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Affiliation(s)
- Em Canh Pham
- Department of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, 700000 Ho Chi Minh city. Vietnam
| | - Tuyen Ngoc Truong
- Department of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, 700000 Ho Chi Minh city. Vietnam
| | - Nguyen Hanh Dong
- Department of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, 700000 Ho Chi Minh city. Vietnam
| | - Duy Duc Vo
- Department of Chemistry, and Department of Cell and Molecular Biology, Uppsala University, Uppsala city. Sweden
| | - Tuoi Thi Hong Do
- Department of Pharmacology, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, 700000 Ho Chi Minh city. Vietnam
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10
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Asad M, Khan SA, Arshad MN, Asiri AM, Rehan M. Design and synthesis of novel pyrazoline derivatives for their spectroscopic, single crystal X-ray and biological studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Baldelli V, D'Angelo F, Pavoncello V, Fiscarelli EV, Visca P, Rampioni G, Leoni L. Identification of FDA-approved antivirulence drugs targeting the Pseudomonas aeruginosa quorum sensing effector protein PqsE. Virulence 2021; 11:652-668. [PMID: 32423284 PMCID: PMC7549961 DOI: 10.1080/21505594.2020.1770508] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ability of the bacterial pathogen Pseudomonas aeruginosa to cause both chronic and acute infections mainly relies on its capacity to finely modulate the expression of virulence factors through a complex network of regulatory circuits, including the pqs quorum sensing (QS) system. While in most QS systems the signal molecule/receptor complexes act as global regulators that modulate the expression of QS-controlled genes, the main effector protein of the pqs system is PqsE. This protein is involved in the synthesis of the QS signal molecules 2-alkyl-4(1H)-quinolones (AQs), but it also modulates the expression of genes involved in virulence factors production and biofilm formation via AQ-independent pathway(s). P. aeruginosa pqsE mutants disclose attenuated virulence in plant and animal infection models, hence PqsE is considered a good target for the development of antivirulence drugs against P. aeruginosa. In this study, the negative regulation exerted by PqsE on its own transcription has been exploited to develop a screening system for the identification of PqsE inhibitors in a library of FDA-approved drugs. This led to the identification of nitrofurazone and erythromycin estolate, two antibiotic compounds that reduce the expression of PqsE-dependent virulence traits and biofilm formation in the model strain P. aeruginosa PAO1 at concentrations far below those affecting the bacterial growth rate. Notably, both drugs reduce the production of the PqsE-controlled virulence factor pyocyanin also in P. aeruginosa strains isolated from cystic fibrosis patients, and do not antagonize the activity of antibiotics commonly used to treat P. aeruginosa infection.
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Affiliation(s)
| | | | | | | | - Paolo Visca
- Department of Science, University Roma Tre , Rome, Italy
| | | | - Livia Leoni
- Department of Science, University Roma Tre , Rome, Italy
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12
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Soukarieh F, Liu R, Romero M, Roberston SN, Richardson W, Lucanto S, Oton EV, Qudus NR, Mashabi A, Grossman S, Ali S, Sou T, Kukavica-Ibrulj I, Levesque RC, Bergström CAS, Halliday N, Mistry SN, Emsley J, Heeb S, Williams P, Cámara M, Stocks MJ. Hit Identification of New Potent PqsR Antagonists as Inhibitors of Quorum Sensing in Planktonic and Biofilm Grown Pseudomonas aeruginosa. Front Chem 2020; 8:204. [PMID: 32432073 PMCID: PMC7213079 DOI: 10.3389/fchem.2020.00204] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/04/2020] [Indexed: 12/11/2022] Open
Abstract
Current treatments for Pseudomonas aeruginosa infections are becoming less effective because of the increasing rates of multi-antibiotic resistance. Pharmacological targeting of virulence through inhibition of quorum sensing (QS) dependent virulence gene regulation has considerable therapeutic potential. In P. aeruginosa, the pqs QS system regulates the production of multiple virulence factors as well as biofilm maturation and is a promising approach for developing antimicrobial adjuvants for combatting drug resistance. In this work, we report the hit optimisation for a series of potent novel inhibitors of PqsR, a key regulator of the pqs system, bearing a 2-((5-methyl-5H-[1,2,4]triazino[5,6-b]indol-3-yl)thio) acetamide scaffold. The initial hit compound 7 (PAO1-L IC50 0.98 ± 0.02 μM, PA14 inactive at 10 μM) was obtained through a virtual screening campaign performed on the PqsR ligand binding domain using the University of Nottingham Managed Chemical Compound Collection. Hit optimisation gave compounds with enhanced potency against strains PAO1-L and PA14, evaluated using P. aeruginosa pqs-based QS bioreporter assays. Compound 40 (PAO1-L IC50 0.25 ± 0.12 μM, PA14 IC50 0.34 ± 0.03 μM) is one of the most potent PqsR antagonists reported showing significant inhibition of P. aeruginosa pyocyanin production and pqs system signaling in both planktonic cultures and biofilms. The co-crystal structure of 40 with the PqsR ligand binding domain revealed the specific binding interactions occurring between inhibitor and this key regulatory protein.
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Affiliation(s)
- Fadi Soukarieh
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,The National Biofilms Innovation Centre, University of Nottingham, Nottingham, United Kingdom
| | - Ruiling Liu
- School of Pharmacy, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Manuel Romero
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,The National Biofilms Innovation Centre, University of Nottingham, Nottingham, United Kingdom
| | - Shaun N Roberston
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,The National Biofilms Innovation Centre, University of Nottingham, Nottingham, United Kingdom
| | - William Richardson
- School of Pharmacy, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Simone Lucanto
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,The National Biofilms Innovation Centre, University of Nottingham, Nottingham, United Kingdom
| | - Eduard Vico Oton
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Naim Ruhul Qudus
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Alaa Mashabi
- School of Pharmacy, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Scott Grossman
- School of Pharmacy, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Sadiqur Ali
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Tomás Sou
- Drug Delivery Group, Department of Pharmacy, Uppsala University, Uppsala, Sweden.,Pharmacometrics Group, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada
| | - Christel A S Bergström
- Drug Delivery Group, Department of Pharmacy, Uppsala University, Uppsala, Sweden.,The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Nigel Halliday
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Shailesh N Mistry
- School of Pharmacy, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Jonas Emsley
- The National Biofilms Innovation Centre, University of Nottingham, Nottingham, United Kingdom.,School of Pharmacy, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Paul Williams
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,The National Biofilms Innovation Centre, University of Nottingham, Nottingham, United Kingdom
| | - Miguel Cámara
- School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,The National Biofilms Innovation Centre, University of Nottingham, Nottingham, United Kingdom
| | - Michael J Stocks
- The National Biofilms Innovation Centre, University of Nottingham, Nottingham, United Kingdom.,School of Pharmacy, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
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13
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Asad M, Arshad MN, Khan SA, Oves M, Khalid M, Asiri AM, Braga AA. Cyclization of chalcones into N-propionyl pyrazolines for their single crystal X-ray, computational and antibacterial studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Aleksic I, Jeremic J, Milivojevic D, Ilic-Tomic T, Šegan S, Zlatović M, Opsenica DM, Senerovic L. N-Benzyl Derivatives of Long-Chained 4-Amino-7-chloro-quionolines as Inhibitors of Pyocyanin Production in Pseudomonas aeruginosa. ACS Chem Biol 2019; 14:2800-2809. [PMID: 31647218 DOI: 10.1021/acschembio.9b00682] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pseudomonas aeruginosa is a leading cause of nosocomial infections that are becoming increasingly difficult to treat due to the occurrence of antibiotic resistant strains. Since P. aeruginosa virulence is controlled through quorum sensing, small molecule treatments inhibiting quorum sensing signaling pathways provide a promising therapeutic option. Consequently, we synthesized a series of N-octaneamino-4-aminoquinoline derivatives to optimize this chemotype's antivirulence activity against P. aeruginosa via inhibition of pyocyanin production. The most potent derivative, which possesses a benzofuran substituent, provided effective inhibition of pyocyanin production (IC50 = 12 μM), biofilm formation (BFIC50 = 50 μM), and motility. Experimentally, the compound's activity is achieved through competitive inhibition of PqsR, and structure-activity data were rationalized using molecular docking studies.
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Affiliation(s)
- Ivana Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - Jelena Jeremic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - Dusan Milivojevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - Tatjana Ilic-Tomic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - Sandra Šegan
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
| | - Mario Zlatović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Dejan M. Opsenica
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
- Center of Excellence in Environmental Chemistry and Engineering, ICTM, University of Belgrade, 11000 Belgrade, Serbia
| | - Lidija Senerovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
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15
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Zender M, Witzgall F, Kiefer A, Kirsch B, Maurer CK, Kany AM, Xu N, Schmelz S, Börger C, Blankenfeldt W, Empting M. Flexible Fragment Growing Boosts Potency of Quorum-Sensing Inhibitors against Pseudomonas aeruginosa Virulence. ChemMedChem 2019; 15:188-194. [PMID: 31709767 PMCID: PMC7004148 DOI: 10.1002/cmdc.201900621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 12/24/2022]
Abstract
Hit-to-lead optimization is a critical phase in drug discovery. Herein, we report on the fragment-based discovery and optimization of 2-aminopyridine derivatives as a novel lead-like structure for the treatment of the dangerous opportunistic pathogen Pseudomonas aeruginosa. We pursue an innovative treatment strategy by interfering with the Pseudomonas quinolone signal (PQS) quorum sensing (QS) system leading to an abolishment of bacterial pathogenicity. Our compounds act on the PQS receptor (PqsR), a key transcription factor controlling the expression of various pathogenicity determinants. In this target-driven approach, we made use of biophysical screening via surface plasmon resonance (SPR) followed by isothermal titration calorimetry (ITC)-enabled enthalpic efficiency (EE) evaluation. Hit optimization then involved growth vector identification and exploitation. Astonishingly, the latter was successfully achieved by introducing flexible linkers rather than rigid motifs leading to a boost in activity on the target receptor and anti-virulence potency.
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Affiliation(s)
- Michael Zender
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Florian Witzgall
- Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Alexander Kiefer
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Benjamin Kirsch
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Christine K Maurer
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Andreas M Kany
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Ningna Xu
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Stefan Schmelz
- Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Carsten Börger
- PharmBioTec GmbH, Science Park 1, 66123, Saarbrücken, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany.,Biotechnology and Bioinformatics, Institute for Biochemistry, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Martin Empting
- Drug Design and Optimization (DDOP), 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 E8.1, 66123, Saarbrücken, Germany
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16
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Design, synthesis, and evaluation of compounds capable of reducing Pseudomonas aeruginosa virulence. Eur J Med Chem 2019; 185:111800. [PMID: 31706639 DOI: 10.1016/j.ejmech.2019.111800] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022]
Abstract
Anti-virulence approaches in the treatment of Pseudomonas aeruginosa (PA)-induced infections have shown clinical potential in multiple in vitro and in vivo studies. However, development of these compounds is limited by several factors, including the lack of molecules capable of penetrating the membrane of gram-negative organisms. Here, we report the identification of novel structurally diverse compounds that inhibit PqsR and LasR-based signaling and diminish virulence factor production and biofilm growth in two clinically relevant strains of P. aeruginosa. It is the first report where potential anti-virulent agents were evaluated for inhibition of several virulence factors of PA. Finally, co-treatment with these inhibitors significantly reduced the production of virulence factors induced by the presence of sub-inhibitory levels of ciprofloxacin. Further, we have analyzed the drug-likeness profile of designed compounds using quantitative estimates of drug-likeness (QED) and confirmed their potential as hit molecules for further development.
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17
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Mellini M, Di Muzio E, D’Angelo F, Baldelli V, Ferrillo S, Visca P, Leoni L, Polticelli F, Rampioni G. In silico Selection and Experimental Validation of FDA-Approved Drugs as Anti-quorum Sensing Agents. Front Microbiol 2019; 10:2355. [PMID: 31649658 PMCID: PMC6796623 DOI: 10.3389/fmicb.2019.02355] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022] Open
Abstract
The emergence of antibiotic resistant bacterial pathogens is increasing at an unprecedented pace, calling for the development of new therapeutic options. Small molecules interfering with virulence processes rather than growth hold promise as an alternative to conventional antibiotics. Anti-virulence agents are expected to decrease bacterial virulence and to pose reduced selective pressure for the emergence of resistance. In the opportunistic pathogen Pseudomonas aeruginosa the expression of key virulence traits is controlled by quorum sensing (QS), an intercellular communication process that coordinates gene expression at the population level. Hence, QS inhibitors represent promising anti-virulence agents against P. aeruginosa. Virtual screenings allow fast and cost-effective selection of target ligands among vast libraries of molecules, thus accelerating the time and limiting the cost of conventional drug-discovery processes, while the drug-repurposing approach is based on the identification of off-target activity of FDA-approved drugs, likely endowed with low cytotoxicity and favorable pharmacological properties. This study aims at combining the advantages of virtual screening and drug-repurposing approaches to identify new QS inhibitors targeting the pqs QS system of P. aeruginosa. An in silico library of 1,467 FDA-approved drugs has been screened by molecular docking, and 5 hits showing the highest predicted binding affinity for the pqs QS receptor PqsR (also known as MvfR) have been selected. In vitro experiments have been performed by engineering ad hoc biosensor strains, which were used to verify the ability of hit compounds to decrease PqsR activity in P. aeruginosa. Phenotypic analyses confirmed the impact of the most promising hit, the antipsychotic drug pimozide, on the expression of P. aeruginosa PqsR-controlled virulence traits. Overall, this study highlights the potential of virtual screening campaigns of FDA-approved drugs to rapidly select new inhibitors of important bacterial functions.
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Affiliation(s)
- Marta Mellini
- Department of Science, University Roma Tre, Rome, Italy
| | | | | | | | | | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Fabio Polticelli
- Department of Science, University Roma Tre, Rome, Italy
- National Institute of Nuclear Physics, Roma Tre Section, Rome, Italy
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18
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Anti-PqsR compounds as next-generation antibacterial agents against Pseudomonas aeruginosa: A review. Eur J Med Chem 2019; 172:26-35. [PMID: 30939351 DOI: 10.1016/j.ejmech.2019.03.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 01/31/2023]
Abstract
Nowadays, due to spreading antibiotic resistance among clinically relevant pathogens, the requirement of novel therapeutic approaches is felt more than ever. One of the alternative strategies is anti-virulence therapy without affecting bacterial growth or viability. In Pseudomonas aeruginosa, an opportunistic human pathogen that exhibits intrinsic multi-drug resistance, both virulence factors' production and biofilm formation depends on its quorum sensing (QS) network. Therefore, targeting the key proteins involved in QS system is an attractive method to overcome P. aeruginosa pathogenicity and resistance. The transcriptional regulator PqsR, also called MvfR, is one of these major proteins which employs 3,4-dihydroxy-2-heptylquinoline (PQS) and 4-hydroxy-2-heptylquinoline (HHQ) as signaling molecules. Reviewing the advances in development of small molecules inhibit this protein, assist to open a new window to smart molecule design that may revolutionize treatment of P. aeruginosa infections.
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19
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Shaaban M, Elgaml A, Habib ESE. Biotechnological applications of quorum sensing inhibition as novel therapeutic strategies for multidrug resistant pathogens. Microb Pathog 2018; 127:138-143. [PMID: 30503958 DOI: 10.1016/j.micpath.2018.11.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/25/2018] [Accepted: 11/26/2018] [Indexed: 02/06/2023]
Abstract
High incidence of antibiotic resistance among bacterial clinical isolates necessitates the discovery of new targets for inhibition of microbial pathogenicity, without stimulation of microbial resistance. This could be achieved by targeting virulence determinants, which cause host damage and disease. Many pathogenic bacteria elaborate signaling molecules for cellular communication. This signaling system is named quorum sensing system (QS), and it is contingent on the bacterial population density and mediated by signal molecules called pheromones or autoinducers (AIs). Bacteria utilize QS to regulate activities and behaviors including competence, conjugation, symbiosis, virulence, motility, sporulation, antibiotic production, and biofilm formation. Hence, targeting bacterial communicating signals and suppression of QS exhibit a fundamental approach for competing microbial communication. In this review, we illustrate the common up to date approaches to utilize QS circuits in pathogenic bacteria, including Vibrio fischeri, Pseudomonas aeruginosa, Escherichia coli and Acinetobacter baumannii, as novel therapeutic targets.
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Affiliation(s)
- Mona Shaaban
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taibah University, Al Madinah Al Munawwarah, 30078, Saudi Arabia; Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, 35516, Egypt
| | - Abdelaziz Elgaml
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, 35516, Egypt; Department of Microbiology, Faculty of Pharmacy, Horus University, New Damietta, 34517, Egypt
| | - El-Sayed E Habib
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taibah University, Al Madinah Al Munawwarah, 30078, Saudi Arabia; Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, 35516, Egypt.
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20
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D'Angelo F, Baldelli V, Halliday N, Pantalone P, Polticelli F, Fiscarelli E, Williams P, Visca P, Leoni L, Rampioni G. Identification of FDA-Approved Drugs as Antivirulence Agents Targeting the pqs Quorum-Sensing System of Pseudomonas aeruginosa. Antimicrob Agents Chemother 2018; 62:e01296-18. [PMID: 30201815 PMCID: PMC6201120 DOI: 10.1128/aac.01296-18] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/01/2018] [Indexed: 12/11/2022] Open
Abstract
The long-term use of antibiotics has led to the emergence of multidrug-resistant bacteria. A promising strategy to combat bacterial infections aims at hampering their adaptability to the host environment without affecting growth. In this context, the intercellular communication system quorum sensing (QS), which controls virulence factor production and biofilm formation in diverse human pathogens, is considered an ideal target. Here, we describe the identification of new inhibitors of the pqs QS system of the human pathogen Pseudomonas aeruginosa by screening a library of 1,600 U.S. Food and Drug Administration-approved drugs. Phenotypic characterization of ad hoc engineered strains and in silico molecular docking demonstrated that the antifungal drugs clotrimazole and miconazole, as well as an antibacterial compound active against Gram-positive pathogens, clofoctol, inhibit the pqs system, probably by targeting the transcriptional regulator PqsR. The most active inhibitor, clofoctol, specifically inhibited the expression of pqs-controlled virulence traits in P. aeruginosa, such as pyocyanin production, swarming motility, biofilm formation, and expression of genes involved in siderophore production. Moreover, clofoctol protected Galleria mellonella larvae from P. aeruginosa infection and inhibited the pqs QS system in P. aeruginosa isolates from cystic fibrosis patients. Notably, clofoctol is already approved for clinical treatment of pulmonary infections caused by Gram-positive bacterial pathogens; hence, this drug has considerable clinical potential as an antivirulence agent for the treatment of P. aeruginosa lung infections.
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Affiliation(s)
| | | | - Nigel Halliday
- Centre for Biomolecular Sciences and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Paolo Pantalone
- Centre for Biomolecular Sciences and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Fabio Polticelli
- Department of Science, University Roma Tre, Rome, Italy
- National Institute of Nuclear Physics, Roma Tre Section, Rome, Italy
| | - Ersilia Fiscarelli
- Laboratory of Cystic Fibrosis Microbiology, Bambino Gesú Hospital, Rome, Italy
| | - Paul Williams
- Centre for Biomolecular Sciences and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
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21
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Schütz C, Empting M. Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers. Beilstein J Org Chem 2018; 14:2627-2645. [PMID: 30410625 PMCID: PMC6204780 DOI: 10.3762/bjoc.14.241] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
The Gram-negative opportunistic pathogen Pseudomonas aeruginosa causes severe nosocomial infections. It uses quorum sensing (QS) to regulate and coordinate population-wide group behaviours in the infection process like concerted secretion of virulence factors. One very important signalling network is the Pseudomonas quinolone signal (PQS) QS. With the aim to devise novel and innovative anti-infectives, inhibitors have been designed to address the various potential drug targets present within pqs QS. These range from enzymes within the biosynthesis cascade of the signal molecules PqsABCDE to the receptor of these autoinducers PqsR (MvfR). This review shortly introduces P. aeruginosa and its pathogenicity traits regulated by the pqs system and highlights the published drug discovery efforts providing insights into the compound binding modes if available. Furthermore, suitability of the individual targets for pathoblocker design is discussed.
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Affiliation(s)
- Christian Schütz
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Saarbrücken, Germany
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22
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Soukarieh F, Williams P, Stocks MJ, Cámara M. Pseudomonas aeruginosa Quorum Sensing Systems as Drug Discovery Targets: Current Position and Future Perspectives. J Med Chem 2018; 61:10385-10402. [PMID: 29999316 DOI: 10.1021/acs.jmedchem.8b00540] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is a serious threat to public health globally, manifested by the frequent emergence of multidrug resistant pathogens that render current chemotherapy inadequate. Health organizations worldwide have recognized the severity of this crisis and implemented action plans to contain its adverse consequences and prolong the utility of conventional antibiotics. Hence, there is a pressing need for new classes of antibacterial agents with novel modes of action. Quorum sensing (QS), a communication system employed by bacterial populations to coordinate virulence gene expression, is a potential target that has been intensively investigated over the past decade. This Perspective will focus on recent advances in targeting the three main quorum sensing systems ( las, rhl, and pqs) of a major opportunistic human pathogen, Pseudomonas aeruginosa, and will specifically evaluate the medicinal chemistry strategies devised to develop QS inhibitors from a drug discovery perspective.
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Affiliation(s)
- Fadi Soukarieh
- School of Life Sciences, Centre for Biomolecular Sciences , University of Nottingham , Nottingham , NG7 2RD , U.K
| | - Paul Williams
- School of Life Sciences, Centre for Biomolecular Sciences , University of Nottingham , Nottingham , NG7 2RD , U.K
| | - Michael J Stocks
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham , NG7 2RD , U.K
| | - Miguel Cámara
- School of Life Sciences, Centre for Biomolecular Sciences , University of Nottingham , Nottingham , NG7 2RD , U.K
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23
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Kamal AAM, Petrera L, Eberhard J, Hartmann RW. Structure-functionality relationship and pharmacological profiles of Pseudomonas aeruginosa alkylquinolone quorum sensing modulators. Org Biomol Chem 2018; 15:4620-4630. [PMID: 28513746 DOI: 10.1039/c7ob00263g] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An important paradigm in anti-infective research is the antivirulence concept. Pathoblockers are compounds which disarm bacteria of their arsenal of virulence factors. PqsR is a transcriptional regulator controlling the production of such factors in Pseudomonas aeruginosa, most prominently pyocyanin. In this work, a series of tool compounds based on the structure of the natural ligand 2-heptyl-4-quinolone (HHQ) were used for probing the structure-functionality relationship. Four different profiles are identified namely agonists, antagonists, inverse agonists and biphasic modulators. Molecular docking studies revealed that each class of the PqsR modulators showed distinctive interactions in the PqsR binding domain. It was found that the substituents in position 3 of the quinolone core act as a switch between the different profiles, according to their ability to donate or accept a hydrogen bond, or form a hydrophobic interaction. Finally, it was shown that only inverse agonists were able to strongly inhibit pyocyanin production.
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Affiliation(s)
- Ahmed A M Kamal
- Helmholtz-Institute for Pharmaceutical Research Saarland, Department of Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
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24
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Soukarieh F, Vico Oton E, Dubern JF, Gomes J, Halliday N, de Pilar Crespo M, Ramírez-Prada J, Insuasty B, Abonia R, Quiroga J, Heeb S, Williams P, Stocks MJ, Cámara M. In Silico and in Vitro-Guided Identification of Inhibitors of Alkylquinolone-Dependent Quorum Sensing in Pseudomonas aeruginosa. Molecules 2018; 23:E257. [PMID: 29382099 PMCID: PMC6017655 DOI: 10.3390/molecules23020257] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/20/2018] [Accepted: 01/20/2018] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic pathogen in cystic fibrosis, wound and nosocomial infections, posing a serious burden to public health, due to its antibiotic resistance. The P. aeruginosa Pseudomonas Quinolone System (pqs) quorum sensing system, driven by the activation of the transcriptional regulator, PqsR (MvfR) by alkylquinolone (AQ) signal molecules, is a key player in the regulation of virulence and a potential target for the development of novel antibacterial agents. In this study, we performed in silico docking analysis, coupled with screening using a P. aeruginosa mCTX::PpqsA-lux chromosomal promoter fusion, to identify a series of new PqsR antagonists. The hit compounds inhibited pyocyanin and alkylquinolone signal molecule production in P. aeruginosa PAO1-L and PA14 strains. The inhibitor Ia, which showed the highest activity in PA14, reduced biofilm formation in PAO1-L and PA14, increasing their sensitivity to tobramycin. Furthermore, the hepatic and plasma stabilities for these compounds were determined in both rat and human in vitro microsomal assays, to gain a further understanding of their therapeutic potential. This work has uncovered a new class of P. aeruginosa PqsR antagonists with potential for hit to lead optimisation in the search for quorum sensing inhibitors for future anti-infective drug discovery programs.
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Affiliation(s)
- Fadi Soukarieh
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (F.S.); (E.V.O.); (J.-F.D.); (J.G.); (N.H.); (S.H.); (P.W.)
| | - Eduard Vico Oton
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (F.S.); (E.V.O.); (J.-F.D.); (J.G.); (N.H.); (S.H.); (P.W.)
| | - Jean-Frédéric Dubern
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (F.S.); (E.V.O.); (J.-F.D.); (J.G.); (N.H.); (S.H.); (P.W.)
| | - Janice Gomes
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (F.S.); (E.V.O.); (J.-F.D.); (J.G.); (N.H.); (S.H.); (P.W.)
| | - Nigel Halliday
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (F.S.); (E.V.O.); (J.-F.D.); (J.G.); (N.H.); (S.H.); (P.W.)
| | - Maria de Pilar Crespo
- Department of Microbiology, Universidad del Valle and Departamento of Biomedical Sciences, Universidad Santiago de Cali, Cali AA 760035, Colombia;
| | - Jonathan Ramírez-Prada
- Department of Chemistry, Universidad del Valle, Cali AA 25360, Colombia; (J.R.-P.); (B.I.); (R.A.); (J.Q.)
| | - Braulio Insuasty
- Department of Chemistry, Universidad del Valle, Cali AA 25360, Colombia; (J.R.-P.); (B.I.); (R.A.); (J.Q.)
| | - Rodrigo Abonia
- Department of Chemistry, Universidad del Valle, Cali AA 25360, Colombia; (J.R.-P.); (B.I.); (R.A.); (J.Q.)
| | - Jairo Quiroga
- Department of Chemistry, Universidad del Valle, Cali AA 25360, Colombia; (J.R.-P.); (B.I.); (R.A.); (J.Q.)
| | - Stephan Heeb
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (F.S.); (E.V.O.); (J.-F.D.); (J.G.); (N.H.); (S.H.); (P.W.)
| | - Paul Williams
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (F.S.); (E.V.O.); (J.-F.D.); (J.G.); (N.H.); (S.H.); (P.W.)
| | - Michael J. Stocks
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Miguel Cámara
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (F.S.); (E.V.O.); (J.-F.D.); (J.G.); (N.H.); (S.H.); (P.W.)
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25
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Bilitewski U, Blodgett JAV, Duhme-Klair AK, Dallavalle S, Laschat S, Routledge A, Schobert R. Chemical and Biological Aspects of Nutritional Immunity-Perspectives for New Anti-Infectives that Target Iron Uptake Systems. Angew Chem Int Ed Engl 2017; 56:14360-14382. [PMID: 28439959 DOI: 10.1002/anie.201701586] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 12/22/2022]
Abstract
Upon bacterial infection, one of the defense mechanisms of the host is the withdrawal of essential metal ions, in particular iron, which leads to "nutritional immunity". However, bacteria have evolved strategies to overcome iron starvation, for example, by stealing iron from the host or other bacteria through specific iron chelators with high binding affinity. Fortunately, these complex interactions between the host and pathogen that lead to metal homeostasis provide several opportunities for interception and, thus, allow the development of novel antibacterial compounds. This Review focuses on iron, discusses recent highlights, and gives some future perspectives which are relevant in the fight against antibiotic resistance.
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Affiliation(s)
- Ursula Bilitewski
- AG Compound Profiling and Screening, Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Joshua A V Blodgett
- Department of Biology, Washington University, St. Louis, MO, 63130-4899, USA
| | | | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, I-20133, Milano, Italy
| | - Sabine Laschat
- Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 7, 0569, Stuttgart, Germany
| | - Anne Routledge
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Rainer Schobert
- Organische Chemie I, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
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26
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Bilitewski U, Blodgett JAV, Duhme-Klair AK, Dallavalle S, Laschat S, Routledge A, Schobert R. Chemische und biologische Aspekte von “Nutritional Immunity” - Perspektiven für neue Antiinfektiva mit Fokus auf bakterielle Eisenaufnahmesysteme. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ursula Bilitewski
- AG Compound Profiling and Screening; Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | | | | | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences; Università degli Studi di Milano; I-20133 Milano Italien
| | - Sabine Laschat
- Institut für Organische Chemie; Universität Stuttgart; Pfaffenwaldring 55, 7 0569 Stuttgart Deutschland
| | - Anne Routledge
- Department of Chemistry; University of York, Heslington; York YO10 5DD Großbritannien
| | - Rainer Schobert
- Organische Chemie I; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
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27
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Allegretta G, Maurer CK, Eberhard J, Maura D, Hartmann RW, Rahme L, Empting M. In-depth Profiling of MvfR-Regulated Small Molecules in Pseudomonas aeruginosa after Quorum Sensing Inhibitor Treatment. Front Microbiol 2017; 8:924. [PMID: 28596760 PMCID: PMC5442231 DOI: 10.3389/fmicb.2017.00924] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/08/2017] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium, which causes opportunistic infections in immuno-compromised individuals. Due to its multiple resistances toward antibiotics, the development of new drugs is required. Interfering with Quorum Sensing (QS), a cell-to-cell communication system, has shown to be highly efficient in reducing P. aeruginosa pathogenicity. One of its QS systems employs Pseudomonas Quinolone Signal (PQS) and 4-hydroxy-2-heptylquinoline (HHQ) as signal molecules. Both activate the transcriptional regulator MvfR (Multiple Virulence Factor Regulator), also called PqsR, driving the production of QS molecules as well as toxins and biofilm formation. The aim of this work was to elucidate the effects of QS inhibitors (QSIs), such as MvfR antagonists and PqsBC inhibitors, on the biosynthesis of the MvfR-regulated small molecules 2′-aminoacetophenone (2-AA), dihydroxyquinoline (DHQ), HHQ, PQS, and 4-hydroxy-2-heptylquinoline-N-oxide (HQNO). The employed synthetic MvfR antagonist fully inhibited pqs small molecule formation showing expected sigmoidal dose-response curves for 2-AA, HQNO, HHQ and PQS. Surprisingly, DHQ levels were enhanced at lower antagonist concentrations followed by a full suppression at higher QSI amounts. This particular bi-phasic profile hinted at the accumulation of a biosynthetic intermediate resulting in the observed overproduction of the shunt product DHQ. Additionally, investigations on PqsBC inhibitors showed a reduction of MvfR natural ligands, while increased 2-AA, DHQ and HQNO levels compared to the untreated cells were detected. Moreover, PqsBC inhibitors did not show any significant effect in PA14 pqsC mutant demonstrating their target selectivity. As 2-AA is important for antibacterial tolerance, the QSIs were evaluated in their capability to attenuate persistence. Indeed, persister cells were reduced along with 2-AA inhibition resulting from MvfR antagonism, but not from PqsBC inhibition. In conclusion, antagonizing MvfR using a dosage capable of fully suppressing this QS system will lead to a favorable therapeutic outcome as DHQ overproduction is avoided and bacterial persistence is reduced.
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Affiliation(s)
- Giuseppe Allegretta
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrücken, Germany
| | - Christine K Maurer
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrücken, Germany
| | - Jens Eberhard
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrücken, Germany
| | - Damien Maura
- Department of Surgery and Department of Microbiology and Immunobiology, Harvard Medical School, BostonMA, United States.,Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, BostonMA, United States.,Shriners Hospitals for Children, BostonMA, United States
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrücken, Germany.,Pharmaceutical and Medicinal Chemistry, Saarland UniversitySaarbrücken, Germany
| | - Laurence Rahme
- Department of Surgery and Department of Microbiology and Immunobiology, Harvard Medical School, BostonMA, United States.,Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, BostonMA, United States.,Shriners Hospitals for Children, BostonMA, United States
| | - Martin Empting
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrücken, Germany
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28
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Kamal AAM, Maurer CK, Allegretta G, Haupenthal J, Empting M, Hartmann RW. Quorum Sensing Inhibitors as Pathoblockers for Pseudomonas aeruginosa Infections: A New Concept in Anti-Infective Drug Discovery. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2017_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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29
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Williams G, Ferenczy GG, Ulander J, Keserű GM. Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery. Drug Discov Today 2016; 22:681-689. [PMID: 27916639 DOI: 10.1016/j.drudis.2016.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/12/2016] [Accepted: 11/24/2016] [Indexed: 01/18/2023]
Abstract
Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions.
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Affiliation(s)
- Glyn Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Johan Ulander
- CVMD Innovative Medicines, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
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30
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Ji C, Sharma I, Pratihar D, Hudson LL, Maura D, Guney T, Rahme LG, Pesci EC, Coleman JP, Tan DS. Designed Small-Molecule Inhibitors of the Anthranilyl-CoA Synthetase PqsA Block Quinolone Biosynthesis in Pseudomonas aeruginosa. ACS Chem Biol 2016; 11:3061-3067. [PMID: 27658001 PMCID: PMC5117135 DOI: 10.1021/acschembio.6b00575] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
The Gram-negative bacterial pathogen Pseudomonas aeruginosa uses three interconnected intercellular
signaling systems regulated
by the transcription factors LasR, RhlR, and MvfR (PqsR), which mediate
bacterial cell–cell communication via small-molecule natural
products and control the production of a variety of virulence factors.
The MvfR system is activated by and controls the biosynthesis of the
quinolone quorum sensing factors HHQ and PQS. A key step in the biosynthesis
of these quinolones is catalyzed by the anthranilyl-CoA synthetase
PqsA. To develop inhibitors of PqsA as novel potential antivirulence
antibiotics, we report herein the design and synthesis of sulfonyladeonsine-based
mimics of the anthranilyl-AMP reaction intermediate that is bound
tightly by PqsA. Biochemical, microbiological, and pharmacological
studies identified two potent PqsA inhibitors, anthranilyl-AMS (1) and anthranilyl-AMSN (2), that decreased HHQ
and PQS production in P. aeruginosa strain
PA14. However, these compounds did not inhibit
production of the virulence factor pyocyanin. Moreover, they exhibited
limited bacterial penetration in compound accumulation studies. This
work provides the most potent PqsA inhibitors reported to date and
sets the stage for future efforts to develop analogues with improved
cellular activity to investigate further the complex relationships
between quinolone biosynthesis and virulence factor production in P. aeruginosa and the therapeutic potential of targeting
PqsA.
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Affiliation(s)
| | | | | | - L. Lynn Hudson
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
| | - Damien Maura
- Department
of Surgery, Harvard Medical School and Massachusettts General Hospital, 50
Blossom Street, Boston, Massachusetts 02114, United States
| | | | - Laurence G. Rahme
- Department
of Surgery, Harvard Medical School and Massachusettts General Hospital, 50
Blossom Street, Boston, Massachusetts 02114, United States
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Shriners Hospitals for
Children Boston, Boston, Massachusetts 02114, United States
| | - Everett C. Pesci
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
| | - James P. Coleman
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
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31
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Thomann A, Brengel C, Börger C, Kail D, Steinbach A, Empting M, Hartmann RW. Structure-Activity Relationships of 2-Sufonylpyrimidines as Quorum-Sensing Inhibitors to Tackle Biofilm Formation and eDNA Release ofPseudomonas aeruginosa. ChemMedChem 2016; 11:2522-2533. [DOI: 10.1002/cmdc.201600419] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/27/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
| | - Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
| | - Carsten Börger
- PharmBioTec GmbH; Science Park 1 66123 Saarbrücken Germany
| | - Dagmar Kail
- PharmBioTec GmbH; Science Park 1 66123 Saarbrücken Germany
| | - Anke Steinbach
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
- Saarland University; Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Campus C 2.3 66123 Saarbrücken Germany
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32
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Zender M, Witzgall F, Drees SL, Weidel E, Maurer CK, Fetzner S, Blankenfeldt W, Empting M, Hartmann RW. Dissecting the Multiple Roles of PqsE in Pseudomonas aeruginosa Virulence by Discovery of Small Tool Compounds. ACS Chem Biol 2016; 11:1755-63. [PMID: 27082157 DOI: 10.1021/acschembio.6b00156] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pseudomonas aeruginosa uses quorum sensing (QS) as a cell-to-cell communication system to orchestrate the expression of virulence determinants. The biosynthesis of the important Pseudomonas quinolone signal (PQS) requires the pqsABCDE operon. Here, PqsE acts as a pathway-specific thioesterase, but it also contributes to the regulation of bacterial virulence via an unknown mechanism. In this manuscript, we report the discovery of PqsE inhibitors as tool compounds to gain further insights into its different functions. Differential scanning fluorimetry (DSF) was used to screen a fragment library, and isothermal titration calorimetry (ITC) was employed as a secondary filter. As proven by X-ray crystallography, hit molecules bound to the active center inhibiting PqsE's thioesterase activity in cell-based and in vitro assays. Notably, the ligands did not affect the levels of the PqsE-regulated virulence factor pyocyanin. These findings indicate that the regulatory function of PqsE is not linked to its thioesterase activity and must be encoded outside of the active center. This study highlights the potential of fragment-based screening for the discovery of tool compounds. This approach provided novel insight into complex biological systems, which could not be obtained by knockout studies.
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Affiliation(s)
- Michael Zender
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
| | - Florian Witzgall
- Helmholtz Centre for Infection Research, Department
Structure and Function of Proteins, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Steffen L. Drees
- Institute
of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany
| | - Elisabeth Weidel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
| | - Christine K. Maurer
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
| | - Susanne Fetzner
- Institute
of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany
| | - Wulf Blankenfeldt
- Helmholtz Centre for Infection Research, Department
Structure and Function of Proteins, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institut
für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
- Pharmaceutical
and Medicinal Chemistry, Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
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33
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Welsh MA, Blackwell HE. Chemical probes of quorum sensing: from compound development to biological discovery. FEMS Microbiol Rev 2016; 40:774-94. [PMID: 27268906 DOI: 10.1093/femsre/fuw009] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 01/20/2023] Open
Abstract
Bacteria can utilize chemical signals to coordinate the expression of group-beneficial behaviors in a method of cell-cell communication called quorum sensing (QS). The discovery that QS controls the production of virulence factors and biofilm formation in many common pathogens has driven an explosion of research aimed at both deepening our fundamental understanding of these regulatory networks and developing chemical agents that can attenuate QS signaling. The inherently chemical nature of QS makes studying these pathways with small molecule tools a complementary approach to traditional microbiology techniques. Indeed, chemical tools are beginning to yield new insights into QS regulation and provide novel strategies to inhibit QS. Here, we review the most recent advances in the development of chemical probes of QS systems in Gram-negative bacteria, with an emphasis on the opportunistic pathogen Pseudomonas aeruginosa We first describe reports of novel small molecule modulators of QS receptors and QS signal synthases. Next, in several case studies, we showcase how chemical tools have been deployed to reveal new knowledge of QS biology and outline lessons for how researchers might best target QS to combat bacterial virulence. To close, we detail the outstanding challenges in the field and suggest strategies to overcome these issues.
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Affiliation(s)
- Michael A Welsh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
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34
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Woods LA, Dolezal O, Ren B, Ryan JH, Peat TS, Poulsen SA. Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination. J Med Chem 2016; 59:2192-204. [PMID: 26882437 DOI: 10.1021/acs.jmedchem.5b01940] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.
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Affiliation(s)
- Lucy A Woods
- Griffith University , Eskitis Institute for Drug Discovery, Brisbane, Queensland Australia
| | - Olan Dolezal
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Bin Ren
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - John H Ryan
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Sally-Ann Poulsen
- Griffith University , Eskitis Institute for Drug Discovery, Brisbane, Queensland Australia
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35
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Wagner S, Sommer R, Hinsberger S, Lu C, Hartmann RW, Empting M, Titz A. Novel Strategies for the Treatment of Pseudomonas aeruginosa Infections. J Med Chem 2016; 59:5929-69. [DOI: 10.1021/acs.jmedchem.5b01698] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Stefanie Wagner
- Chemical
Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
| | - Roman Sommer
- Chemical
Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
| | - Stefan Hinsberger
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
- Drug
Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
| | - Cenbin Lu
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
- Drug
Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
- Drug
Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
| | - Martin Empting
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
- Drug
Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
| | - Alexander Titz
- Chemical
Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
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36
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Reuter K, Steinbach A, Helms V. Interfering with Bacterial Quorum Sensing. PERSPECTIVES IN MEDICINAL CHEMISTRY 2016; 8:1-15. [PMID: 26819549 PMCID: PMC4718088 DOI: 10.4137/pmc.s13209] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/22/2023]
Abstract
Quorum sensing (QS) describes the exchange of chemical signals in bacterial populations to adjust the bacterial phenotypes according to the density of bacterial cells. This serves to express phenotypes that are advantageous for the group and ensure bacterial survival. To do so, bacterial cells synthesize autoinducer (AI) molecules, release them to the environment, and take them up. Thereby, the AI concentration reflects the cell density. When the AI concentration exceeds a critical threshold in the cells, the AI may activate the expression of virulence-associated genes or of luminescent proteins. It has been argued that targeting the QS system puts less selective pressure on these pathogens and should avoid the development of resistant bacteria. Therefore, the molecular components of QS systems have been suggested as promising targets for developing new anti-infective compounds. Here, we review the QS systems of selected gram-negative and gram-positive bacteria, namely, Vibrio fischeri, Pseudomonas aeruginosa, and Staphylococcus aureus, and discuss various antivirulence strategies based on blocking different components of the QS machinery.
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Affiliation(s)
- Kerstin Reuter
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.; Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Anke Steinbach
- Department of Drug Design and Optimization, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
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37
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Niu P, Kang J, Tian X, Song L, Liu H, Wu J, Yu W, Chang J. Synthesis of 2-amino-1,3,4-oxadiazoles and 2-amino-1,3,4-thiadiazoles via sequential condensation and I2-mediated oxidative C–O/C–S bond formation. J Org Chem 2015; 80:1018-24. [PMID: 25506709 DOI: 10.1021/jo502518c] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
2-Amino-substituted 1,3,4-oxadiazoles and 1,3,4-thiadiazoles were synthesized via condensation of semicarbazide/thiosemicarbazide and the corresponding aldehydes followed by I2-mediated oxidative C–O/C–S bond formation. This transition-metal-free sequential synthesis process is compatible with aromatic, aliphatic, and cinnamic aldehydes, providing facile access to a variety of diazole derivatives bearing a 2-amino substituent in an efficient and scalable fashion.
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38
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Ji F, Li X, Guo W, Wu W, Jiang H. Palladium-Catalyzed Oxidative O–H/N–H Carbonylation of Hydrazides: Access to Substituted 1,3,4-Oxadiazole-2(3H)-ones. J Org Chem 2015; 80:5713-8. [DOI: 10.1021/acs.joc.5b00664] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Fanghua Ji
- School of Chemistry and Chemical
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Xianwei Li
- School of Chemistry and Chemical
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Wei Guo
- School of Chemistry and Chemical
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Wanqing Wu
- School of Chemistry and Chemical
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Huanfeng Jiang
- School of Chemistry and Chemical
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
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39
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Pirard B, Ertl P. Evaluation of a semi-automated workflow for fragment growing. J Chem Inf Model 2015; 55:180-93. [PMID: 25514394 DOI: 10.1021/ci5006355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intelligent Automatic Design (IADE) is an expert system developed at Novartis to identify nonclassical bioisosteres. In addition to bioisostere searching, one could also use IADE to grow a fragment bound to a protein. Here we report an evaluation of IADE as a tool for fragment growing. Three examples from the literature served as test cases. In all three cases, IADE generated close analogues of the published compounds and reproduced their crystallographic binding modes. This exercise validated the use of the IADE system for fragment growing. We have also gained experience in optimizing the performance of IADE for this type of application.
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Affiliation(s)
- Bernard Pirard
- Novartis Institutes for BioMedical Research , Novartis Campus, CH-4056 Basel, Switzerland
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40
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Rampioni G, Leoni L, Williams P. The art of antibacterial warfare: Deception through interference with quorum sensing–mediated communication. Bioorg Chem 2014; 55:60-8. [DOI: 10.1016/j.bioorg.2014.04.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 01/02/2023]
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41
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Alkaloids: an overview of their antibacterial, antibiotic-enhancing and antivirulence activities. Int J Antimicrob Agents 2014; 44:377-86. [PMID: 25130096 DOI: 10.1016/j.ijantimicag.2014.06.001] [Citation(s) in RCA: 336] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 06/20/2014] [Indexed: 11/22/2022]
Abstract
With reports of pandrug-resistant bacteria causing untreatable infections, the need for new antibacterial therapies is more pressing than ever. Alkaloids are a large and structurally diverse group of compounds that have served as scaffolds for important antibacterial drugs such as metronidazole and the quinolones. In this review, we highlight other alkaloids with development potential. Natural, semisynthetic and synthetic alkaloids of all classes are considered, looking first at those with direct antibacterial activity and those with antibiotic-enhancing activity. Potent examples include CJ-13,136, a novel actinomycete-derived quinolone alkaloid with a minimum inhibitory concentration of 0.1 ng/mL against Helicobacter pylori, and squalamine, a polyamine alkaloid from the dogfish shark that renders Gram-negative pathogens 16- to >32-fold more susceptible to ciprofloxacin. Where available, information on toxicity, structure-activity relationships, mechanisms of action and in vivo activity is presented. The effects of alkaloids on virulence gene regulatory systems such as quorum sensing and virulence factors such as sortases, adhesins and secretion systems are also described. The synthetic isoquinoline alkaloid virstatin, for example, inhibits the transcriptional regulator ToxT in Vibrio cholerae, preventing expression of cholera toxin and fimbriae and conferring in vivo protection against intestinal colonisation. The review concludes with implications and limitations of the described research and directions for future research.
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42
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Nafee N, Husari A, Maurer CK, Lu C, de Rossi C, Steinbach A, Hartmann RW, Lehr CM, Schneider M. Antibiotic-free nanotherapeutics: ultra-small, mucus-penetrating solid lipid nanoparticles enhance the pulmonary delivery and anti-virulence efficacy of novel quorum sensing inhibitors. J Control Release 2014; 192:131-40. [PMID: 24997276 DOI: 10.1016/j.jconrel.2014.06.055] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 12/18/2022]
Abstract
Cystic fibrosis (CF) is a genetic disease mainly manifested in the respiratory tract. Pseudomonas aeruginosa (P. aeruginosa) is the most common pathogen identified in cultures of the CF airways, however, its eradication with antibiotics remains challenging as it grows in biofilms that counterwork human immune response and dramatically decrease susceptibility to antibiotics. P. aeruginosa regulates pathogenicity via a cell-to-cell communication system known as quorum sensing (QS) involving the virulence factor (pyocyanin), thus representing an attractive target for coping with bacterial pathogenicity. The first in vivo potent QS inhibitor (QSI) was recently developed. Nevertheless, its lipophilic nature might hamper its penetration of non-cellular barriers such as mucus and bacterial biofilms, which limits its biomedical application. Successful anti-infective inhalation therapy necessitates proper design of a biodegradable nanocarrier allowing: 1) high loading and prolonged release, 2) mucus penetration, 3) effective pulmonary delivery, and 4) maintenance of the anti-virulence activity of the QSI. In this context, various pharmaceutical lipids were used to prepare ultra-small solid lipid nanoparticles (us-SLNs) by hot melt homogenization. Plain and QSI-loaded SLNs were characterized in terms of colloidal properties, drug loading, in vitro release and acute toxicity on Calu-3 cells. Mucus penetration was studied using a newly-developed confocal microscopy technique based on 3D-time-lapse imaging. For pulmonary application, nebulization efficiency of SLNs and lung deposition using next generation impactor (NGI) were performed. The anti-virulence efficacy was investigated by pyocyanin formation in P. aeruginosa cultures. Ultra-small SLNs (<100nm diameter) provided high encapsulation efficiency (68-95%) according to SLN composition, high burst in phosphate buffer saline compared to prolonged release of the payload over >8h in simulated lung fluid with minor burst. All types and concentrations of plain and QSI-loaded SLNs maintained the viability of Calu-3 cells. 3D time-lapse confocal imaging proved the ability of SLNs to penetrate into artificial sputum model. SLNs were efficiently nebulized; NGI experiments revealed their deposition in the bronchial region. Overall, nanoencapsulated QSI showed up to sevenfold superior anti-virulence activity to the free compound. Most interestingly, the plain SLNs exhibited anti-virulence properties themselves, which was shown to be related to anti-virulence effects of the emulsifiers used. These startling findings represent a new perspective of ultimate significance in the area of nano-based delivery of novel anti-infectives.
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Affiliation(s)
- Noha Nafee
- Pharmaceutics and Biopharmacy, Philipps University Marburg, Marburg, Germany; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Delivery (DDEL), Saarland University, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany; Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt.
| | - Ayman Husari
- Pharmaceutics and Biopharmacy, Philipps University Marburg, Marburg, Germany; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Delivery (DDEL), Saarland University, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Christine K Maurer
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Development and Optimization (DDOP), Saarland University, Saarbrücken, Germany
| | - Cenbin Lu
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Development and Optimization (DDOP), Saarland University, Saarbrücken, Germany
| | - Chiara de Rossi
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Delivery (DDEL), Saarland University, Saarbrücken, Germany
| | - Anke Steinbach
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Development and Optimization (DDOP), Saarland University, Saarbrücken, Germany
| | - Rolf W Hartmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Development and Optimization (DDOP), Saarland University, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Delivery (DDEL), Saarland University, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Marc Schneider
- Pharmaceutics and Biopharmacy, Philipps University Marburg, Marburg, Germany.
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43
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Hutter MC, Brengel C, Negri M, Henn C, Zimmer C, Hartmann RW, Empting M, Steinbach A. Mechanistic details for anthraniloyl transfer in PqsD: the initial step in HHQ biosynthesis. J Mol Model 2014; 20:2255. [PMID: 24842325 DOI: 10.1007/s00894-014-2255-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/21/2014] [Indexed: 11/25/2022]
Abstract
PqsD mediates the conversion of anthraniloyl-coenzyme A (ACoA) to 2-heptyl-4-hydroxyquinoline (HHQ), a precursor of the Pseudomonas quinolone signal (PQS) molecule. Due to the role of the quinolone signaling pathway of Pseudomonas aeruginosa in the expression of several virulence factors and biofilm formation, PqsD is a potential target for controlling this nosocomial pathogen, which exhibits a low susceptibility to standard antibiotics. PqsD belongs to the β-ketoacyl-ACP synthase family and is similar in structure to homologous FabH enzymes in E. coli and Mycobacterium tuberculosis. Here, we used molecular dynamics simulations to obtain the structural position of the substrate ACoA in the binding pocket of PqsD, and semiempirical molecular orbital calculations to study the reaction mechanism for the catalytic cleavage of ACoA. Our findings suggest a nucleophilic attack of the deprotonated sulfur of Cys112 at the carbonyl carbon of ACoA and a switch in the protonation pattern of His257 whereby Nδ is protonated and the proton of Nε is shifted to the sulfur of CoA during the reaction. This is in agreement with the experimentally determined decreased catalytic activity of the Cys112Ser mutant, whereas the Cys112Ala, His257Phe, and Asn287Ala mutants are all inactive. ESI mass-spectrometric measurements of the Asn287Ala mutant show that anthraniloyl remains covalently bound to Cys112, thus further supporting the inference from our computed mechanism that Asn287 does not take part in the cleavage of ACoA. Since this mutant is inactive, we suggest instead that Asn287 must play an essential role in the subsequent formation of HHQ in vitro.
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Affiliation(s)
- Michael C Hutter
- Center for Bioinformatics, Saarland University, Campus Building E2.1, 66123, Saarbrücken, Germany,
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44
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Optimization of anti-virulence PqsR antagonists regarding aqueous solubility and biological properties resulting in new insights in structure–activity relationships. Eur J Med Chem 2014; 79:173-83. [DOI: 10.1016/j.ejmech.2014.04.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 04/03/2014] [Accepted: 04/04/2014] [Indexed: 12/28/2022]
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45
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Francis CL, Kenny PW, Dolezal O, Saubern S, Kruger M, Savage GP, Peat TS, Ryan JH. Construction of the CSIRO Fragment Library. Aust J Chem 2013. [DOI: 10.1071/ch13325] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A fundamental component of a successful fragment screening program is a productive fragment library, one that delivers hit fragments with potential for pharmaceutical development. A proprietary fragment library was developed by identifying and extracting subsets of CSIRO’s Compound Collection using two complimentary approaches. Over time, the use of surface plasmon resonance as a front-line screening tool has enabled identification and exclusion of problematic compounds and led to a more reliable fragment screening library.
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