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Hetta HF, Ramadan YN, Rashed ZI, Alharbi AA, Alsharef S, Alkindy TT, Alkhamali A, Albalawi AS, Battah B, Donadu MG. Quorum Sensing Inhibitors: An Alternative Strategy to Win the Battle against Multidrug-Resistant (MDR) Bacteria. Molecules 2024; 29:3466. [PMID: 39124871 PMCID: PMC11313800 DOI: 10.3390/molecules29153466] [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: 05/07/2024] [Revised: 06/29/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Antibiotic resistance is a major problem and a major global health concern. In total, there are 16 million deaths yearly from infectious diseases, and at least 65% of infectious diseases are caused by microbial communities that proliferate through the formation of biofilms. Antibiotic overuse has resulted in the evolution of multidrug-resistant (MDR) microbial strains. As a result, there is now much more interest in non-antibiotic therapies for bacterial infections. Among these revolutionary, non-traditional medications is quorum sensing inhibitors (QSIs). Bacterial cell-to-cell communication is known as quorum sensing (QS), and it is mediated by tiny diffusible signaling molecules known as autoinducers (AIs). QS is dependent on the density of the bacterial population. QS is used by Gram-negative and Gram-positive bacteria to control a wide range of processes; in both scenarios, QS entails the synthesis, identification, and reaction to signaling chemicals, also known as auto-inducers. Since the usual processes regulated by QS are the expression of virulence factors and the creation of biofilms, QS is being investigated as an alternative solution to antibiotic resistance. Consequently, the use of QS-inhibiting agents, such as QSIs and quorum quenching (QQ) enzymes, to interfere with QS seems like a good strategy to prevent bacterial infections. This review sheds light on QS inhibition strategy and mechanisms and discusses how using this approach can aid in winning the battle against resistant bacteria.
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Affiliation(s)
- Helal F. Hetta
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.A.); (S.A.); (T.T.A.)
| | - Yasmin N. Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt; (Y.N.R.); (Z.I.R.)
| | - Zainab I. Rashed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt; (Y.N.R.); (Z.I.R.)
| | - Ahmad A. Alharbi
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.A.); (S.A.); (T.T.A.)
| | - Shomokh Alsharef
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.A.); (S.A.); (T.T.A.)
| | - Tala T. Alkindy
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.A.); (S.A.); (T.T.A.)
| | - Alanoud Alkhamali
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.); (A.S.A.)
| | - Abdullah S. Albalawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.); (A.S.A.)
| | - Basem Battah
- Department of Biochemistry and Microbiology, Faculty of Pharmacy, Antioch Syrian Private University, Maaret Siadnaya 22734, Syria
| | - Matthew G. Donadu
- Hospital Pharmacy, Giovanni Paolo II Hospital, ASL Gallura, 07026 Olbia, Italy;
- Department of Medicine, Surgery and Pharmacy, Scuola di Specializzazione in Farmacia Ospedaliera, University of Sassari, 07100 Sassari, Italy
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D’Aquila P, De Rose E, Sena G, Scorza A, Cretella B, Passarino G, Bellizzi D. Quorum Quenching Approaches against Bacterial-Biofilm-Induced Antibiotic Resistance. Antibiotics (Basel) 2024; 13:619. [PMID: 39061301 PMCID: PMC11273524 DOI: 10.3390/antibiotics13070619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
With the widespread phenomenon of antibiotic resistance and the diffusion of multiple drug-resistant bacterial strains, enormous efforts are being conducted to identify suitable alternative agents against pathogenic microorganisms. Since an association between biofilm formation and antibiotic resistance phenotype has been observed, a promising strategy pursued in recent years focuses on controlling and preventing this formation by targeting and inhibiting the Quorum Sensing (QS) system, whose central role in biofilm has been extensively demonstrated. Therefore, the research and development of Quorum Quenching (QQ) compounds, which inhibit QS, has gradually attracted the attention of researchers and has become a new strategy for controlling harmful microorganisms. Among these, a number of both natural and synthetic compounds have been progressively identified as able to interrupt the intercellular communication within a microbial community and the adhesion to a surface, thus disintegrating mature/preformed biofilms. This review describes the role played by QS in the formation of bacterial biofilms and then focuses on the mechanisms of different natural and synthetic QS inhibitors (QSIs) exhibiting promising antibiofilm ability against Gram-positive and Gram-negative bacterial pathogens and on their applications as biocontrol strategies in various fields.
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Affiliation(s)
- Patrizia D’Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (P.D.); (E.D.R.); (G.S.); (G.P.)
| | - Elisabetta De Rose
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (P.D.); (E.D.R.); (G.S.); (G.P.)
| | - Giada Sena
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (P.D.); (E.D.R.); (G.S.); (G.P.)
| | - Angelo Scorza
- Villa Ermelinda, Progetto Terza Età, 88842 Cutro, Italy; (A.S.); (B.C.)
| | | | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (P.D.); (E.D.R.); (G.S.); (G.P.)
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (P.D.); (E.D.R.); (G.S.); (G.P.)
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3
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Shi Q, Wen H, Xu Y, Zhao X, Zhang J, Li Y, Meng Q, Yu F, Xiao J, Li X. Virtual screening-based discovery of AI-2 quorum sensing inhibitors that interact with an allosteric hydrophobic site of LsrK and their functional evaluation. Front Chem 2023; 11:1185224. [PMID: 37292175 PMCID: PMC10244669 DOI: 10.3389/fchem.2023.1185224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction: Quorum sensing (QS) is a bacterial intracellular and intercellular communication system that regulates virulence factor production, biofilm formation, and antibiotic sensitivity. Quorum-sensing inhibitors (QSIs) are a novel class of antibiotics that can effectively combat antibiotic resistance. Autoinducer-2 (AI-2) is a universal signaling molecule that mediates inter- and intraspecies QS systems among different bacteria. Furthermore, LsrK plays an important role in regulating the activity and stability of the intracellular AI-2 signaling pathway. Thus, LsrK is considered an important target for the development of QSIs. Methods: We designed a workflow integrating molecular dynamic (MD) simulations, virtual screening, LsrK inhibition assays, cell-based AI-2-mediated QS interference assays, and surface plasmon resonance (SPR)-based protein affinity assays to screen for potential LsrK kinase inhibitors. Results: MD simulation results of the LsrK/ATP complex revealed hydrogen bonds and salt bridge formation among four key residues, namely, Lys 431, Tyr 341, Arg 319, and Arg 322, which are critical for the binding of ATP to LsrK. Furthermore, MD simulation results indicated that the ATP-binding site has an allosteric pocket that can become larger and be occupied by small molecule compounds. Based on these MD simulation results, a constraint of forming at least one hydrogen bond with Arg 319, Arg 322, Lys 431, or Tyr 341 residues was introduced when performing virtual screening using Glide's virtual screening workflow (VSW). In the meantime, compounds with hydrophobic group likely to interact with the allosteric hydrophobic pocket are preferred when performing visual inspection. Seventy-four compounds were selected for the wet laboratory assays based on virtual screening and the absorption, distribution, metabolism, and excretion (ADME) properties of these compounds. LsrK inhibition assays revealed 12 compounds inhibiting LsrK by more than 60% at a 200 μM concentration; four of these (Y205-6768, D135-0149, 3284-1358, and N025-0038) had IC50 values below 50 μM and were confirmed as ATP-competitive inhibitors. Six of these 12 LsrK inhibitors exhibited high AI-2 QS inhibition, of which, Y205-6768 had the highest activity with IC50 = 11.28 ± 0.70 μM. The SPR assay verified that compounds Y205-6768 and N025-0038 specifically bound to LsrK. MD simulation analysis of the docking complexes of the four active compounds with LsrK further confirmed the importance of forming hydrogen bonds and salt bridges with key basic amino acid residues including Lys 431, Tyr 341, Arg 319, and Arg 322 and filling the allosteric hydrophobic pocket next to the purine-binding site of LsrK. Discussion: Our study clarified for the first time that there is an allosteric site near the ATP-binding site of Lsrk and that it enriches the structure-activity relationship information of Lsrk inhibitors. The four identified compounds showed novel structures, low molecular weights, high activities, and novel LsrK binding modes, rendering them suitable for further optimization for effective AI-2 QSIs. Our work provides a valuable reference for the discovery of QSIs that do not inhibit bacterial growth, thereby avoiding the emergence of drug resistance.
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Affiliation(s)
- Qianqian Shi
- School of Petrochemical Engineering, Liaoning Petrochemical University, Fushun, China
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yijie Xu
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xu Zhao
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jing Zhang
- Qionglai Medical Center Hospital, Chengdu, China
| | - Ye Li
- The No 968 Hospital of PLA, Jinzhou, China
| | - Qingbin Meng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Fang Yu
- School of Petrochemical Engineering, Liaoning Petrochemical University, Fushun, China
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Junhai Xiao
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xingzhou Li
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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Xu Y, Zeng C, Wen H, Shi Q, Zhao X, Meng Q, Li X, Xiao J. Discovery of AI-2 Quorum Sensing Inhibitors Targeting the LsrK/HPr Protein-Protein Interaction Site by Molecular Dynamics Simulation, Virtual Screening, and Bioassay Evaluation. Pharmaceuticals (Basel) 2023; 16:ph16050737. [PMID: 37242520 DOI: 10.3390/ph16050737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Quorum sensing (QS) is a cell-to-cell communication mechanism that regulates bacterial pathogenicity, biofilm formation, and antibiotic sensitivity. Among the identified quorum sensing, AI-2 QS exists in both Gram-negative and Gram-positive bacteria and is responsible for interspecies communication. Recent studies have highlighted the connection between the phosphotransferase system (PTS) and AI-2 QS, with this link being associated with protein-protein interaction (PPI) between HPr and LsrK. Here, we first discovered several AI-2 QSIs targeting the LsrK/HPr PPI site through molecular dynamics (MD) simulation, virtual screening, and bioassay evaluation. Of the 62 compounds purchased, eight compounds demonstrated significant inhibition in LsrK-based assays and AI-2 QS interference assays. Surface plasmon resonance (SPR) analysis confirmed that the hit compound 4171-0375 specifically bound to the LsrK-N protein (HPr binding domain, KD = 2.51 × 10-5 M), and therefore the LsrK/HPr PPI site. The structure-activity relationships (SARs) emphasized the importance of hydrophobic interactions with the hydrophobic pocket and hydrogen bonds or salt bridges with key residues of LsrK for LsrK/HPr PPI inhibitors. These new AI-2 QSIs, especially 4171-0375, exhibited novel structures, significant LsrK inhibition, and were suitable for structural modification to search for more effective AI-2 QSIs.
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Affiliation(s)
- Yijie Xu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Chunlan Zeng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Qianqian Shi
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Xu Zhao
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Qingbin Meng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Xingzhou Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Junhai Xiao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
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Meng F, Zhang F, Chen Q, Yang M, Yang Y, Li X, Gu W, Yu J. Virtual screening and in vitro experimental verification of LuxS inhibitors from natural products for Lactobacillus reuteri. Biomed Pharmacother 2022; 147:112521. [PMID: 35149360 DOI: 10.1016/j.biopha.2021.112521] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/02/2022] Open
Abstract
The rapid proliferation and colonization of probiotics in the intestines are essential for human health. Quorum sensing (QS) is a communication mechanism among bacteria, which can regulate various bacterial crowd behavior. This study aimed to enhance the viability of Lactobacillus reuteri 1-12 by regulating QS. Herein, we built a database containing 72 natural products (previously reported) that can improve intestinal flora. Virtual screening (VS) was subsequently conducted to screen four potential active compounds. After that, molecular docking was conducted to analyze the binding mode of the four natural products to S-Ribosylhomocysteinase (LuxS). The results showed that norathyriol, mangiferin, baicalein, and kaempferol had good binding ability to LuxS. The validation experiment showed that norathyriol, mangiferin, baicalein, and kaempferol could inhibit the production of autoinducer-2 (AI-2). Moreover, mangiferin significantly increased L. reuteri 1-12 biomass and promoted L. reuteri 1-12 biofilm formation and structure. Besides, only mangiferin inhibited luxS expression, thus increasing L. reuteri 1-12 biomass. This research indicated that mangiferin may be a potential inhibitor of LuxS, promoting the probiotic properties of L. reuteri and human health.
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Affiliation(s)
- Fanying Meng
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Fan Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Qiuding Chen
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Min Yang
- Kunming Third People's Hospital, 319 Wujing Road, Guandu District, Kunming, Yunnan, China
| | - Yaqin Yang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Xue Li
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Wen Gu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China.
| | - Jie Yu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China.
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Lamin A, Kaksonen AH, Cole IS, Chen XB. Quorum sensing inhibitors applications: a new prospect for mitigation of microbiologically influenced corrosion. Bioelectrochemistry 2022; 145:108050. [DOI: 10.1016/j.bioelechem.2022.108050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 12/21/2022]
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Medarametla P, Kronenberger T, Laitinen T, Poso A. Structural Characterization of LsrK as a Quorum Sensing Target and a Comparison between X-ray and Homology Models. J Chem Inf Model 2021; 61:1346-1353. [PMID: 33683884 PMCID: PMC8028047 DOI: 10.1021/acs.jcim.0c01233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Quorum sensing is
being investigated as an alternative therapeutic
strategy in antibacterial drug discovery programs aimed at combatting
bacterial resistance. LsrK is an autoinducer-2 kinase (belongs to
the sugar kinase family), playing a key role in the phosphorylation
of the autoinducer-2 (AI-2) signaling molecules involved in quorum
sensing. Inhibiting LsrK could result in reduced pathogenicity by
interfering with quorum sensing signaling. Previously, we have generated
homology models to employ in structure-based virtual screening and
successfully identified the first class of LsrK inhibitors. While
conducting these studies, the crystal structure of LsrK was released,
providing us with an opportunity to evaluate the reliability and quality
of our models. A comparative structural analysis of the crystal structure
and homology models revealed consistencies among them in the overall
structural fold and binding site. Furthermore, the binding characteristics
and conformational changes of LsrK have been investigated using molecular
dynamics to inspect whether LsrK undergoes similar conformational
changes as that of sugar kinases. These studies revealed the flexibility
of the LsrK C-terminal domain (Domain II) attributing to the conformational
changes in LsrK resulting in open and closed states during the phosphorylation.
Further, simulations provided us with insights into the flexibility
of a loop in Domain I that can influence the ligand accessibility
to the LsrK binding site.
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Affiliation(s)
- Prasanthi Medarametla
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.,Department of Oncology and Pneumonology, Internal Medicine, University Hospital Tübingen, Otfried-Müller-Straße 10, DE 72076 Tübingen, Germany
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.,Department of Oncology and Pneumonology, Internal Medicine, University Hospital Tübingen, Otfried-Müller-Straße 10, DE 72076 Tübingen, Germany
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Linciano P, Cavalloro V, Martino E, Kirchmair J, Listro R, Rossi D, Collina S. Tackling Antimicrobial Resistance with Small Molecules Targeting LsrK: Challenges and Opportunities. J Med Chem 2020; 63:15243-15257. [PMID: 33152241 PMCID: PMC8016206 DOI: 10.1021/acs.jmedchem.0c01282] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance (AMR) is a growing threat with severe health and economic consequences. The available antibiotics are losing efficacy, and the hunt for alternative strategies is a priority. Quorum sensing (QS) controls biofilm and virulence factors production. Thus, the quenching of QS to prevent pathogenicity and to increase bacterial susceptibility to antibiotics is an appealing therapeutic strategy. The phosphorylation of autoinducer-2 (a mediator in QS) by LsrK is a crucial step in triggering the QS cascade. Thus, LsrK represents a valuable target in fighting AMR. Few LsrK inhibitors have been reported so far, allowing ample room for further exploration. This perspective aims to provide a comprehensive analysis of the current knowledge about the structural and biological properties of LsrK and the state-of-the-art technology for LsrK inhibitor design. We elaborate on the challenges in developing novel LsrK inhibitors and point out promising avenues for further research.
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Affiliation(s)
- Pasquale Linciano
- Department
of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Valeria Cavalloro
- Department
of Earth and Environmental Science, University
of Pavia, Via Sant’Epifanio 14, 27100 Pavia, Italy
| | - Emanuela Martino
- Department
of Earth and Environmental Science, University
of Pavia, Via Sant’Epifanio 14, 27100 Pavia, Italy
| | - Johannes Kirchmair
- Department
of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Roberta Listro
- Department
of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department
of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Simona Collina
- Department
of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
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Tiwari PB, Chapagain PP, Seddek A, Annamalai T, Üren A, Tse-Dinh YC. Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. ChemMedChem 2020; 15:623-631. [PMID: 32043806 PMCID: PMC7133791 DOI: 10.1002/cmdc.201900721] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/11/2022]
Abstract
A topoisomerase-DNA transient covalent complex can be a druggable target for novel topoisomerase poison inhibitors that represent a new class of antibacterial or anticancer drugs. Herein, we have investigated molecular features of the functionally important Escherichia coli topoisomerase I (EctopoI)-DNA covalent complex (EctopoIcc) for molecular simulations, which is very useful in the development of new antibacterial drugs. To demonstrate the usefulness of our approach, we used a model small molecule (SM), NSC76027, obtained from virtual screening. We examined the direct binding of NSC76027 to EctopoI as well as inhibition of EctopoI relaxation activity of this SM via experimental techniques. We then performed molecular dynamics (MD) simulations to investigate the dynamics and stability of EctopoIcc and EctopoI-NSC76027-DNA ternary complex. Our simulation results show that NSC76027 forms a stable ternary complex with EctopoIcc. EctopoI investigated here also serves as a model system for investigating a complex of topoisomerase and DNA in which DNA is covalently attached to the protein.
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Affiliation(s)
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
| | - Ahmed Seddek
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Thirunavukkarasu Annamalai
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC 20057, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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10
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Gatta V, Tomašič T, Ilaš J, Zidar N, Peterlin Mašič L, Barančoková M, Frlan R, Anderluh M, Kikelj D, Tammela P. A New Cell-Based AI-2-Mediated Quorum Sensing Interference Assay in Screening of LsrK-Targeted Inhibitors. Chembiochem 2020; 21:1918-1922. [PMID: 32026533 DOI: 10.1002/cbic.201900773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 01/06/2023]
Abstract
Quorum sensing (QS), a bacterial communication strategy, has been recognized as one of the control mechanisms of virulence in bacteria. Thus, targeting QS offers an interesting opportunity to impair bacterial pathogenicity and develop antivirulence agents. Aiming to enhance the discovery of QS inhibitors, we developed a bioreporter Escherichia coli JW5505 pET-Plsrlux and set up a cell-based assay for identifying inhibitors of autoinducer-2 (AI-2)-mediated QS. A comparative study on the performance of target- versus cell-based assays was performed, and 91 compounds selected with the potential to target the ATP binding pocket of LsrK, a key enzyme in AI-2 processing, were tested in an LsrK inhibition assay, providing 36 hits. The same set of compounds was tested by the AI-2-mediated QS interference assay, resulting in 24 active compounds. Among those, six were also found to be active against LsrK, whereas 18 might target other components of the pathway. Thus, this AI-2-mediated QS interference cell-based assay is an effective tool for complementing target-based assays, yet also stands as an independent assay for primary screening.
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Affiliation(s)
- Viviana Gatta
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014, Helsinki, Finland
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Michaela Barančoková
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Rok Frlan
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Marko Anderluh
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014, Helsinki, Finland
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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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Targeting Quorum Sensing: High-Throughput Screening to Identify Novel LsrK Inhibitors. Int J Mol Sci 2019; 20:ijms20123112. [PMID: 31242708 PMCID: PMC6627609 DOI: 10.3390/ijms20123112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022] Open
Abstract
Since quorum sensing (QS) is linked to the establishment of bacterial infection, its inactivation represents one of the newest strategies to fight bacterial pathogens. LsrK is a kinase playing a key role in the processing of autoinducer-2 (AI-2), a quorum-sensing mediator in gut enteric bacteria. Inhibition of LsrK might thus impair the quorum-sensing cascade and consequently reduce bacterial pathogenicity. Aiming for the development of a target-based assay for the discovery of LsrK inhibitors, we evaluated different assay set-ups based on ATP detection and optimized an automation-compatible method for the high-throughput screening of chemical libraries. The assay was then used to perform the screening of a 2000-compound library, which provided 12 active compounds with an IC50 ≤ 10 µM confirming the effectiveness and sensitivity of our assay. Follow-up studies on the positive hits led to the identification of two compounds, harpagoside and rosolic acid, active in a cell-based AI-2 QS interference assay, which are at the moment the most promising candidates for the development of a new class of antivirulence agents based on LsrK inhibition.
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