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Manisha Y, Srinivasan M, Jobichen C, Rosenshine I, Sivaraman J. Sensing for survival: specialised regulatory mechanisms of Type III secretion systems in Gram-negative pathogens. Biol Rev Camb Philos Soc 2024; 99:837-863. [PMID: 38217090 DOI: 10.1111/brv.13047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/15/2024]
Abstract
For centuries, Gram-negative pathogens have infected the human population and been responsible for numerous diseases in animals and plants. Despite advancements in therapeutics, Gram-negative pathogens continue to evolve, with some having developed multi-drug resistant phenotypes. For the successful control of infections caused by these bacteria, we need to widen our understanding of the mechanisms of host-pathogen interactions. Gram-negative pathogens utilise an array of effector proteins to hijack the host system to survive within the host environment. These proteins are secreted into the host system via various secretion systems, including the integral Type III secretion system (T3SS). The T3SS spans two bacterial membranes and one host membrane to deliver effector proteins (virulence factors) into the host cell. This multifaceted process has multiple layers of regulation and various checkpoints. In this review, we highlight the multiple strategies adopted by these pathogens to regulate or maintain virulence via the T3SS, encompassing the regulation of small molecules to sense and communicate with the host system, as well as master regulators, gatekeepers, chaperones, and other effectors that recognise successful host contact. Further, we discuss the regulatory links between the T3SS and other systems, like flagella and metabolic pathways including the tricarboxylic acid (TCA) cycle, anaerobic metabolism, and stringent cell response.
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Affiliation(s)
- Yadav Manisha
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Mahalashmi Srinivasan
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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2
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Manson DE, Ananiev GE, Guo S, Ericksen SS, Santa EE, Blackwell HE. Abiotic Small Molecule Inhibitors and Activators of the LasR Quorum Sensing Receptor in Pseudomonas aeruginosa with Potencies Comparable or Surpassing N-Acyl Homoserine Lactones. ACS Infect Dis 2024; 10:1212-1221. [PMID: 38506163 PMCID: PMC11014758 DOI: 10.1021/acsinfecdis.3c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa controls almost 10% of its genome, including myriad virulence genes, via a cell-to-cell chemical communication system called quorum sensing (QS). Small molecules that either inhibit or activate QS in P. aeruginosa represent useful research tools to study the role of this signaling pathway in infection and interrogate its viability as an antivirulence target. However, despite active research in this area over the past 20+ years, there are relatively few synthetic compounds known to strongly inhibit or activate QS in P. aeruginosa. Most reported QS modulators in this pathogen are of low potency or have structural liabilities that limit their application in biologically relevant environments such as mimics of the native N-acyl l-homoserine lactone (AHL) signals. Here, we report the results of a high-throughput screen for abiotic small molecules that target LasR, a key QS regulator in P. aeruginosa. We screened a 25,000-compound library and discovered four new structural classes of abiotic LasR modulators. These compounds include antagonists that surpass the potency of all known AHL-type compounds and mimetics thereof, along with an agonist with potency approaching that of LasR's native ligand. The novel structures of this compound set, along with their anticipated robust physicochemical profiles, underscore their potential value as probe molecules to interrogate the roles of QS in this formidable pathogen.
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Affiliation(s)
- Daniel E Manson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Gene E Ananiev
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Song Guo
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Spencer S Ericksen
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Emma E Santa
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
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3
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Alasiri A, Soltane R, Taha MN, Abd El-Aleam RH, Alshehri F, Sayed AM. Bakuchiol inhibits Pseudomonas aeruginosa's quorum sensing-dependent biofilm formation by selectively inhibiting its transcriptional activator protein LasR. Int J Biol Macromol 2024; 255:128025. [PMID: 37979739 DOI: 10.1016/j.ijbiomac.2023.128025] [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: 08/06/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023]
Abstract
In the present study, we characterized Bakuchiol (Bak) as a new potent quorum sensing (QS) inhibitor against Pseudomonas aeruginosa biofilm formation. Upon extensive in vitro investigations, Bak was found to suppress the P. aeruginosa biofilm formation (75.5 % inhibition) and its associated virulence factor e.g., pyocyanin and rhamnolipids (% of inhibition = 71.5 % and 66.9 %, respectively). Upon LuxR-type receptors assay, Bak was found to selectively inhibit P. aeruginosa's LasR in a dose-dependent manner. Further in-depth molecular investigations (e.g., sedimentation velocity and thermal shift assays) revealed that Bak destabilized LasR upon binding and disrupted its functioning quaternary structure (i.e., the functioning dimeric form). The subsequent modeling and molecular dynamics (MD) simulations explained in more molecular detail how Bak interacts with LasR and how it can induce its dimeric form disruption. In conclusion, our study identified Bak as a potent and specific LasR antagonist that should be widely used as a chemical probe of QS in P. aeruginosa, offering new insights into LasR antagonism processes. The new findings shed light on the cryptic world of LuxR-type QS in this important opportunistic pathogen.
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Affiliation(s)
- Ahlam Alasiri
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Mostafa N Taha
- Microbiology and Immunology Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.
| | - Rehab H Abd El-Aleam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information MTI, Cairo 11571, Egypt.
| | - Fatma Alshehri
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Ahmed M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni Suef, Egypt; Department of Pharmacognosy, College of Pharmacy, Almaaqal University, 61014 Basra, Iraq.
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4
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Koh CMM, Ping LSY, Xuan CHH, Theng LB, San HS, Palombo EA, Wezen XC. A data-driven machine learning approach for discovering potent LasR inhibitors. Bioengineered 2023; 14:2243416. [PMID: 37552115 PMCID: PMC10411317 DOI: 10.1080/21655979.2023.2243416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
The rampant spread of multidrug-resistant Pseudomonas aeruginosa strains severely threatens global health. This severity is compounded against the backdrop of a stagnating antibiotics development pipeline. Moreover, with many promising therapeutics falling short of expectations in clinical trials, targeting the las quorum sensing (QS) system remains an attractive therapeutic strategy to combat P. aeruginosa infection. Thus, our primary goal was to develop a drug prediction algorithm using machine learning to identify potent LasR inhibitors. In this work, we demonstrated using a Multilayer Perceptron (MLP) algorithm boosted with AdaBoostM1 to discriminate between active and inactive LasR inhibitors. The optimal model performance was evaluated using 5-fold cross-validation and test sets. Our best model achieved a 90.7% accuracy in distinguishing active from inactive LasR inhibitors, an area under the Receiver Operating Characteristic Curve value of 0.95, and a Matthews correlation coefficient value of 0.81 when evaluated using test sets. Subsequently, we deployed the model against the Enamine database. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies, Molecular Dynamics simulations, MM-GBSA analysis, and Free Energy Landscape analysis. Our data indicate that several of our chosen top hits showed better ligand-binding affinities than naringenin, a competitive LasR inhibitor. Among the six top hits, five of these compounds were predicted to be LasR inhibitors that could be used to treat P. aeruginosa-associated infections. To our knowledge, this study provides the first assessment of using an MLP-based QSAR model for discovering potent LasR inhibitors to attenuate P. aeruginosa infections.
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Affiliation(s)
- Christabel Ming Ming Koh
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Lilian Siaw Yung Ping
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Christopher Ha Heng Xuan
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Lau Bee Theng
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Hwang Siaw San
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Enzo A. Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Xavier Chee Wezen
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
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5
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Keegan NR, Colón Torres NJ, Stringer AM, Prager LI, Brockley MW, McManaman CL, Wade JT, Paczkowski JE. Promoter selectivity of the RhlR quorum-sensing transcription factor receptor in Pseudomonas aeruginosa is coordinated by distinct and overlapping dependencies on C4-homoserine lactone and PqsE. PLoS Genet 2023; 19:e1010900. [PMID: 38064526 PMCID: PMC10732425 DOI: 10.1371/journal.pgen.1010900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/20/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
Quorum sensing is a mechanism of bacterial cell-cell communication that relies on the production and detection of small molecule autoinducers, which facilitate the synchronous expression of genes involved in group behaviors, such as virulence factor production and biofilm formation. The Pseudomonas aeruginosa quorum sensing network consists of multiple interconnected transcriptional regulators, with the transcription factor, RhlR, acting as one of the main drivers of quorum sensing behaviors. RhlR is a LuxR-type transcription factor that regulates its target genes when bound to its cognate autoinducer, C4-homoserine lactone, which is synthesized by RhlI. RhlR function is also regulated by the metallo-β-hydrolase enzyme, PqsE. We recently showed that PqsE binds RhlR to alter its affinity for promoter DNA, a new mechanism of quorum-sensing receptor activation. Here, we perform ChIP-seq analyses of RhlR to map the binding of RhlR across the P. aeruginosa genome, and to determine the impact of C4-homoserine lactone and PqsE on RhlR binding to different sites across the P. aeruginosa genome. We identify 40 RhlR binding sites, all but three of which are associated with genes known to be regulated by RhlR. C4-homoserine lactone is required for maximal binding of RhlR to many of its DNA sites. Moreover, C4-homoserine lactone is required for maximal RhlR-dependent transcription activation from all sites, regardless of whether it impacts RhlR binding to DNA. PqsE is required for maximal binding of RhlR to many DNA sites, with similar effects on RhlR-dependent transcription activation from those sites. However, the effects of PqsE on RhlR specificity are distinct from those of C4-homoserine lactone, and PqsE is sufficient for RhlR binding to some DNA sites in the absence of C4-homoserine lactone. Together, C4-homoserine lactone and PqsE are required for RhlR binding at the large majority of its DNA sites. Thus, our work reveals three distinct modes of activation by RhlR: i) when RhlR is unbound by autoinducer but bound by PqsE, ii) when RhlR is bound by autoinducer but not bound by PqsE, and iii) when RhlR is bound by both autoinducer and PqsE, establishing a stepwise mechanism for the progression of the RhlR-RhlI-PqsE quorum sensing pathway in P. aeruginosa.
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Affiliation(s)
- Nicholas R. Keegan
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
| | - Nathalie J. Colón Torres
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Anne M. Stringer
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Lia I. Prager
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biological Sciences, University at Albany, Albany, New York, United States of America
| | - Matthew W. Brockley
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biological Sciences, University at Albany, Albany, New York, United States of America
| | - Charity L. McManaman
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Jon E. Paczkowski
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
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Soltane R, Alasiri A, Taha MN, Abd El-Aleam RH, Alghamdi KS, Ghareeb MA, Keshek DEG, Cardoso SM, Sayed AM. Norlobaridone Inhibits Quorum Sensing-Dependent Biofilm Formation and Some Virulence Factors in Pseudomonas aeruginosa by Disrupting Its Transcriptional Activator Protein LasR Dimerization. Biomolecules 2023; 13:1573. [PMID: 38002255 PMCID: PMC10669572 DOI: 10.3390/biom13111573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/26/2023] Open
Abstract
In the present study, norlobaridone (NBD) was isolated from Parmotrema and then evaluated as a new potent quorum sensing (QS) inhibitor against Pseudomonas aeruginosa biofilm development. This phenolic natural product was found to reduce P. aeruginosa biofilm formation (64.6% inhibition) and its related virulence factors, such as pyocyanin and rhamnolipids (% inhibition = 61.1% and 55%, respectively). In vitro assays inhibitory effects against a number of known LuxR-type receptors revealed that NBD was able to specifically block P. aeruginosa's LasR in a dose-dependent manner. Further molecular studies (e.g., sedimentation velocity and thermal shift assays) demonstrated that NBD destabilized LasR upon binding and damaged its functional quaternary structure (i.e., the functional dimeric form). The use of modelling and molecular dynamics (MD) simulations also allowed us to further understand its interaction with LasR, and how this can disrupt its dimeric form. Finally, our findings show that NBD is a powerful and specific LasR antagonist that should be widely employed as a chemical probe in QS of P. aeruginosa, providing new insights into LasR antagonism processes. The new discoveries shed light on the mysterious world of LuxR-type QS in this key opportunistic pathogen.
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Affiliation(s)
- Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Ahlam Alasiri
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Mostafa N. Taha
- Microbiology and Immunology Department, Faculty of Pharmacy, Nahda University, Beni-Suef 62764, Egypt;
| | - Rehab H. Abd El-Aleam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo 11571, Egypt;
| | - Kawthar Saad Alghamdi
- Department of Biology, College of Science, University of Hafr Al Batin, Hafar Al Batin 39511, Saudi Arabia;
| | - Mosad A. Ghareeb
- Medicinal Chemistry Department, Theodor Bilharz Research Institute Kornaish El Nile, Warrak El-Hadar, Imbaba, P.O. Box 30, Giza 12411, Egypt;
| | - Doaa El-Ghareeb Keshek
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
- Agriculture Genetic Engineering Research Institute (AGERI), Agriculture Research Center, Giza 11571, Egypt
| | - Susana M. Cardoso
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Ahmed M. Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
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7
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Ballante F, Turkina MV, Ntzouni M, Magnusson KE, Vikström E. Modified N-acyl-L-homoserine lactone compounds abrogate Las-dependent quorum-sensing response in human pathogen Pseudomonas aeruginosa. Front Mol Biosci 2023; 10:1264773. [PMID: 37908228 PMCID: PMC10613653 DOI: 10.3389/fmolb.2023.1264773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
Quorum sensing (QS) is a mode of cell-cell communication that bacteria use to sense population density and orchestrate collective behaviors. The common opportunistic human pathogen Pseudomonas aeruginosa employs QS to regulate a large set of genes involved in virulence and host-pathogen interactions. The Las circuit positioned on the top of the QS hierarchy in P. aeruginosa makes use of N-acyl-L-homoserine lactones (AHLs) as signal molecules, like N-3-oxo-dodecanoyl-L-homoserine lactone (3O-C12-HSL). Disabling QS circuits by certain small-molecule compounds, known as quorum-sensing inhibitors (QSIs), has been proposed as a strategy to attenuate bacterial pathogenicity. In this study, four new AHL analogs were designed by incorporating a tert-butoxycarbonyl Boc group in amide and β-keto (3-oxo) moiety. Compounds were evaluated on a molecular and phenotypic basis as a QSI using the screening strategy linked to the assignment of the Las QS system in P. aeruginosa. Using a LasR-based bioreporter, we found that the compounds decreased LasR-controlled light activity and competed efficiently with natural 3O-C12-HSL. The compounds reduced the production of the cognate 3O-C12-HSL and certain virulence traits, like total protease activity, elastase activity, pyocyanin production, and extracellular DNA release. Furthermore, a quantitative proteomic approach was used to study the effect of the compounds on QS-regulated extracellular proteins. Among the four compounds tested, one of them showed the most significant difference in the appearance of the 3O-C12-HSL-responsive reference proteins related to QS communication and virulence, i.e., a distinct activity as a QSI. Moreover, by combining experimental data with computational chemistry, we addressed the effect of LasR protein flexibility on docking precision and assessed the advantage of using a multi-conformational docking procedure for binding mode prediction of LasR modulators. Thus, the four new AHL compounds were tested for their interaction with the AHL-binding site in LasR to identify the key interferences with the activity of LasR. Our study provides further insight into molecular features that are required for small-molecule modulation of LasR-dependent QS communication in P. aeruginosa. This should facilitate rational design of the next generation of antivirulence tools to study and manipulate QS-controlled fitness in bacteria and, thereby, handle bacterial infections in a new way.
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Affiliation(s)
- Flavio Ballante
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Maria V. Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Maria Ntzouni
- Core Facility, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Karl-Eric Magnusson
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Elena Vikström
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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Ghosh M, Raghav S, Ghosh P, Maity S, Mohela K, Jain D. Structural analysis of novel drug targets for mitigation of Pseudomonas aeruginosa biofilms. FEMS Microbiol Rev 2023; 47:fuad054. [PMID: 37771093 DOI: 10.1093/femsre/fuad054] [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: 05/30/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 09/30/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen responsible for acute and chronic, hard to treat infections. Persistence of P. aeruginosa is due to its ability to develop into biofilms, which are sessile bacterial communities adhered to substratum and encapsulated in layers of self-produced exopolysaccharides. These biofilms provide enhanced protection from the host immune system and resilience towards antibiotics, which poses a challenge for treatment. Various strategies have been expended for combating biofilms, which involve inhibiting biofilm formation or promoting their dispersal. The current remediation approaches offer some hope for clinical usage, however, treatment and eradication of preformed biofilms is still a challenge. Thus, identifying novel targets and understanding the detailed mechanism of biofilm regulation becomes imperative. Structure-based drug discovery (SBDD) provides a powerful tool that exploits the knowledge of atomic resolution details of the targets to search for high affinity ligands. This review describes the available structural information on the putative target protein structures that can be utilized for high throughput in silico drug discovery against P. aeruginosa biofilms. Integrating available structural information on the target proteins in readily accessible format will accelerate the process of drug discovery.
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Affiliation(s)
- Moumita Ghosh
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Shikha Raghav
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Puja Ghosh
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Swagatam Maity
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Kavery Mohela
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Deepti Jain
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
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9
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Kanak KR, Dass RS, Pan A. Anti-quorum sensing potential of selenium nanoparticles against LasI/R, RhlI/R, and PQS/MvfR in Pseudomonas aeruginosa: a molecular docking approach. Front Mol Biosci 2023; 10:1203672. [PMID: 37635941 PMCID: PMC10449602 DOI: 10.3389/fmolb.2023.1203672] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Pseudomonas aeruginosa is an infectious pathogen which has the ability to cause primary and secondary contagions in the blood, lungs, and other body parts of immunosuppressed individuals, as well as community-acquired diseases, such as folliculitis, osteomyelitis, pneumonia, and others. This opportunistic bacterium displays drug resistance and regulates its pathogenicity via the quorum sensing (QS) mechanism, which includes the LasI/R, RhlI/R, and PQS/MvfR systems. Targeting the QS systems might be an excellent way to treat P. aeruginosa infections. Although a wide array of antibiotics, namely, newer penicillins, cephalosporins, and combination drugs are being used, the use of selenium nanoparticles (SeNPs) to cure P. aeruginosa infections is extremely rare as their mechanistic interactions are weakly understood, which results in carrying out this study. The present study demonstrates a computational approach of binding the interaction pattern between SeNPs and the QS signaling proteins in P. aeruginosa, utilizing multiple bioinformatics approaches. The computational investigation revealed that SeNPs were acutely 'locked' into the active region of the relevant proteins by the abundant residues in their surroundings. The PatchDock-based molecular docking analysis evidently indicated the strong and significant interaction between SeNPs and the catalytic cleft of LasI synthase (Phe105-Se = 2.7 Å and Thr121-Se = 3.8 Å), RhlI synthase (Leu102-Se = 3.7 Å and Val138-Se = 3.2 Å), transcriptional receptor protein LasR (Lys42-Se = 3.9 Å, Arg122-Se = 3.2 Å, and Glu124-Se = 3.9 Å), RhlR (Tyr43-Se = 2.9 Å, Tyr45-Se = 3.4 Å, and His61-Se = 3.5 Å), and MvfR (Leu208-Se = 3.2 Å and Arg209-Se = 4.0 Å). The production of acyl homoserine lactones (AHLs) was inhibited by the use of SeNPs, thereby preventing QS as well. Obstructing the binding affinity of transcriptional regulatory proteins may cause the suppression of LasR, RhlR, and MvfR systems to become inactive, thereby blocking the activation of QS-regulated virulence factors along with their associated gene expression. Our findings clearly showed that SeNPs have anti-QS properties against the established QS systems of P. aeruginosa, which strongly advocated that SeNPs might be a potent solution to tackle drug resistance and a viable alternative to conventional antibiotics along with being helpful in therapeutic development to cure P. aeruginosa infections.
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Affiliation(s)
- Kanak Raj Kanak
- Fungal Genetics and Mycotoxicology Laboratory, Department of Microbiology, School of Life Sciences, Pondicherry University (A Central University), Pondicherry, India
| | - Regina Sharmila Dass
- Fungal Genetics and Mycotoxicology Laboratory, Department of Microbiology, School of Life Sciences, Pondicherry University (A Central University), Pondicherry, India
| | - Archana Pan
- Department of Bioinformatics, School of Life Sciences, Pondicherry University (A Central University), Pondicherry, India
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10
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Miller Conrad LC, Perez LJ. A Geneticist Transcribing the Chemical Language of Bacteria. Isr J Chem 2023; 63:e202200079. [PMID: 37469628 PMCID: PMC10353724 DOI: 10.1002/ijch.202200079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 12/05/2022]
Abstract
The study of quorum sensing, bacterial cell-to-cell communication mediated by the production and detection of small molecule signals, has skyrocketed since its discovery in the last third of the 20th century. Building from early investigations of bacterial bioluminescence, the process has been characterized to control a numerous and growing number of group behaviors, including virulence and biofilm formation. Bonnie Bassler has made key contributions to the understanding of quorum sensing, leading interdisciplinary efforts to characterize key signaling pathway components and their respective signaling molecules across a range of gram-negative bacteria. This review highlights her work in the field, with a particular emphasis on the chemical contributions of her work.
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Affiliation(s)
- Laura C. Miller Conrad
- Department of Chemistry, San José State University, 1 Washington Sq, San Jose, CA 95192, USA
| | - Lark J. Perez
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
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11
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Feathers JR, Richael EK, Simanek KA, Fromme JC, Paczkowski JE. Structure of the RhlR-PqsE complex from Pseudomonas aeruginosa reveals mechanistic insights into quorum-sensing gene regulation. Structure 2022; 30:1626-1636.e4. [PMID: 36379213 PMCID: PMC9722607 DOI: 10.1016/j.str.2022.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for thousands of deaths every year in the United States. P. aeruginosa virulence factor production is mediated by quorum sensing, a mechanism of bacterial cell-cell communication that relies on the production and detection of signal molecules called autoinducers. In P. aeruginosa, the transcription factor receptor RhlR is activated by a RhlI-synthesized autoinducer. We recently showed that RhlR-dependent transcription is enhanced by a physical interaction with the enzyme PqsE via increased affinity of RhlR for promoter DNA. However, the molecular basis for complex formation and how complex formation enhanced RhlR transcriptional activity remained unclear. Here, we report the structure of ligand-bound RhlR in complex with PqsE. Additionally, we determined the structure of the complex bound with DNA, revealing the mechanism by which RhlR-mediated transcription is enhanced by PqsE, thereby establishing the molecular basis for RhlR-dependent virulence factor production in P. aeruginosa.
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Affiliation(s)
- J Ryan Feathers
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Erica K Richael
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Kayla A Simanek
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY 12201, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jon E Paczkowski
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY 12201, USA.
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12
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Borgert SR, Henke S, Witzgall F, Schmelz S, Zur Lage S, Hotop SK, Stephen S, Lübken D, Krüger J, Gomez NO, van Ham M, Jänsch L, Kalesse M, Pich A, Brönstrup M, Häussler S, Blankenfeldt W. Moonlighting chaperone activity of the enzyme PqsE contributes to RhlR-controlled virulence of Pseudomonas aeruginosa. Nat Commun 2022; 13:7402. [PMID: 36456567 PMCID: PMC9715718 DOI: 10.1038/s41467-022-35030-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Pseudomonas aeruginosa is a major cause of nosocomial infections and also leads to severe exacerbations in cystic fibrosis or chronic obstructive pulmonary disease. Three intertwined quorum sensing systems control virulence of P. aeruginosa, with the rhl circuit playing the leading role in late and chronic infections. The majority of traits controlled by rhl transcription factor RhlR depend on PqsE, a dispensable thioesterase in Pseudomonas Quinolone Signal (PQS) biosynthesis that interferes with RhlR through an enigmatic mechanism likely involving direct interaction of both proteins. Here we show that PqsE and RhlR form a 2:2 protein complex that, together with RhlR agonist N-butanoyl-L-homoserine lactone (C4-HSL), solubilizes RhlR and thereby renders the otherwise insoluble transcription factor active. We determine crystal structures of the complex and identify residues essential for the interaction. To corroborate the chaperone-like activity of PqsE, we design stability-optimized variants of RhlR that bypass the need for C4-HSL and PqsE in activating PqsE/RhlR-controlled processes of P. aeruginosa. Together, our data provide insight into the unique regulatory role of PqsE and lay groundwork for developing new P. aeruginosa-specific pharmaceuticals.
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Affiliation(s)
- Sebastian Roman Borgert
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Steffi Henke
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Florian Witzgall
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Stefan Schmelz
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Susanne Zur Lage
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Sven-Kevin Hotop
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Steffi Stephen
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Dennis Lübken
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Jonas Krüger
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Nicolas Oswaldo Gomez
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Marco van Ham
- Cellular Proteomics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Markus Kalesse
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Andreas Pich
- Institute for Toxicology, Core Facility Proteomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Mark Brönstrup
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Susanne Häussler
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany.
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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13
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Abd El-Aleam RH, Sayed AM, Taha MN, George RF, Georgey HH, Abdel-Rahman HM. Design and synthesis of novel benzimidazole derivatives as potential Pseudomonas aeruginosa anti-biofilm agents inhibiting LasR: Evidence from comprehensive molecular dynamics simulation and in vitro investigation. Eur J Med Chem 2022; 241:114629. [DOI: 10.1016/j.ejmech.2022.114629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/10/2022] [Accepted: 07/21/2022] [Indexed: 11/04/2022]
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Resistance Is Not Futile: The Role of Quorum Sensing Plasticity in Pseudomonas aeruginosa Infections and Its Link to Intrinsic Mechanisms of Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10061247. [PMID: 35744765 PMCID: PMC9228389 DOI: 10.3390/microorganisms10061247] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 01/01/2023] Open
Abstract
Bacteria use a cell-cell communication process called quorum sensing (QS) to orchestrate collective behaviors. QS relies on the group-wide detection of extracellular signal molecules called autoinducers (AI). Quorum sensing is required for virulence and biofilm formation in the human pathogen Pseudomonas aeruginosa. In P. aeruginosa, LasR and RhlR are homologous LuxR-type soluble transcription factor receptors that bind their cognate AIs and activate the expression of genes encoding functions required for virulence and biofilm formation. While some bacterial signal transduction pathways follow a linear circuit, as phosphoryl groups are passed from one carrier protein to another ultimately resulting in up- or down-regulation of target genes, the QS system in P. aeruginosa is a dense network of receptors and regulators with interconnecting regulatory systems and outputs. Once activated, it is not understood how LasR and RhlR establish their signaling hierarchy, nor is it clear how these pathway connections are regulated, resulting in chronic infection. Here, we reviewed the mechanisms of QS progression as it relates to bacterial pathogenesis and antimicrobial resistance and tolerance.
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GÜRAĞAÇ DERELİ FT, ÖNEM E, ÖZAYDIN AG, ARIN E, MUHAMMED MT. Persea americana Mill.: As a potent quorum sensing inhibitor of Pseudomonas aeruginosa PAO1 virulence. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2022. [DOI: 10.21448/ijsm.1029610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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16
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Aflakian F, Rad M, Hashemitabar G, Lagzian M, Ramezani M. Design and assessment of novel synthetic peptides to inhibit quorum sensing-dependent biofilm formation in Pseudomonas aeruginosa. BIOFOULING 2022; 38:131-146. [PMID: 35067121 DOI: 10.1080/08927014.2022.2028280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/01/2022] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Pseudomonas aeruginosa is one of the most common biofilm-producing bacteria, often leading to long-term and chronic infections. The LasR regulator protein acts as the central regulator of the quorum sensing (QS) system and coordinates the expression of some virulence and biofilm genes. In this study, novel peptides (WSF, FASK, YDVD) were designed for binding to the domain of the transcriptional activator of the LasR protein and interfere with LasR in the QS system of P. aeruginosa. The effects of these peptides on biofilm production, expression of biofilm-related genes (AlgC, PslA, PelA), and growth of planktonic P. aeruginosa were investigated. All three peptides inhibited the growth of P. aeruginosa planktonic cells at 1600 µg ml-1 and exhibited anti-biofilm effects at sub-inhibitory concentrations (800 µg ml-1). Measurements of the mRNA levels of biofilm-related genes at sub-inhibitory concentrations of the designed peptides showed a significant decrease.
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Affiliation(s)
- Fatemeh Aflakian
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mehrnaz Rad
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Gholamreza Hashemitabar
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Milad Lagzian
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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17
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Escobar-Muciño E. The role of eugenol and ferulic acid as the competitive inhibitors of transcriptional regulator RhlR in P. aeruginosa. MethodsX 2022; 9:101771. [PMID: 35800985 PMCID: PMC9253908 DOI: 10.1016/j.mex.2022.101771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/19/2022] [Indexed: 11/28/2022] Open
Abstract
Search inhibitors of Quorum Sensing (QS) in Pseudomonas aeruginosa are challenging to find therapies due to the broad antibiotic resistance. Therefore, this study aimed to probe ten aromatic compounds as inhibitors of three transcriptional regulators of QS in P. aeruginosa. The methodology consisted in determining the Binding Gibbs Energy (BGE) with software Chimera (tool vina) and Mcule, comparing the averages by the Tukey method (p≤0.05) to find inhibitors of QS. Subsequently, the LD50 in the mice model was evaluated by three QSAR models, and the in silico pharmacokinetic values were obtained from the ADME (the absorption distribution metabolism excretion) and PubChem databases. Found three potential inhibitors of RhlR with the lower BGE values in the range -6.70±0.21 to -7.43±0.35 kcal/mol. On the other side, all compounds were acceptable for Lipinski's rule of fives and the in silico oral mice LD50 and ADME values. Concluding, the ferulic acid and eugenol showed the best total BGE values (-75.07±0.892 and -70.36±1.022 kcal/mol), proposing them as a new therapy against the virulence of P. aeruginosa. Finally, the in silico studies have demonstrated are reproducible and valuable for putative QS inhibitors predicting and obtaining new studies derivatives from the results obtained in the present study. • The key benefits of this methodology are: Use free, licensed, flexible, and efficient software for in silico molecular docking. • Validation and comparison of BGE employing two molecular docking software in three different proteins. • Use classical molecular dynamics to define the stability and the total BGE of interaction protein-ligand and find the best inhibitor of a protein for proposing them as a possible therapy against the virulence of specific pathogens.
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18
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Victoria-Muñoz F, Sánchez-Cruz N, Medina-Franco JL, Lopez-Vallejo F. Cheminformatics analysis of molecular datasets of transcription factors associated with quorum sensing in Pseudomonas aeruginosa. RSC Adv 2022; 12:6783-6790. [PMID: 35424595 PMCID: PMC8981735 DOI: 10.1039/d1ra08352j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/20/2022] [Indexed: 11/21/2022] Open
Abstract
There are molecular structural features that are key to defining the agonist or antagonist activity on LasR, RhlR and PqsR transcription factors, associated with quorum sensing in Pseudomonas aeruginosa.
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Affiliation(s)
- Felipe Victoria-Muñoz
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Farmacia, Av. Cra 30 # 45-03, Bogotá D.C., 11001 Colombia
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Química, Grupo de Investigación en Productos Naturales Vegetales Bioactivos, Av. Cra 30 # 45-03, Bogotá D.C., 11001 Colombia
| | - Norberto Sánchez-Cruz
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510 Mexico
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510 Mexico
| | - Fabian Lopez-Vallejo
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Química, Grupo de Investigación en Productos Naturales Vegetales Bioactivos, Av. Cra 30 # 45-03, Bogotá D.C., 11001 Colombia
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19
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Lou Y, Chang W, Cui T, Wang J, Qian H, Ma L, Hao X, Zhang D. Microbiologically influenced corrosion inhibition mechanisms in corrosion protection: A review. Bioelectrochemistry 2021; 141:107883. [PMID: 34246844 DOI: 10.1016/j.bioelechem.2021.107883] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 01/08/2023]
Abstract
Microbial activities can change the properties of biofilm/metal interfaces to accelerate or decelerate the corrosion of metals in a given environment. Microbiologically influenced corrosion inhibition (MICI) is the inhibition of corrosion that is directly or indirectly induced by microbial action. Compared with conventional methods for protection from corrosion, MICI is environmentally friendly and an emerging approach for the prevention and treatment of (bio)corrosion. However, due to the diversity of microorganisms and the fact that their metabolic processes are greatly complicated by environmental factors, MICI is still facing challenges for practical application. This review provides a comprehensive overview of the mechanisms of MICI under different conditions and their advantages and disadvantages for potential applications in corrosion protection.
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Affiliation(s)
- Yuntian Lou
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Weiwei Chang
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Tianyu Cui
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jinke Wang
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hongchang Qian
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; BRI Southeast Asia Network for Corrosion and Protection (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan 528399, China
| | - Lingwei Ma
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; BRI Southeast Asia Network for Corrosion and Protection (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan 528399, China
| | - Xiangping Hao
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; BRI Southeast Asia Network for Corrosion and Protection (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan 528399, China.
| | - Dawei Zhang
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China; BRI Southeast Asia Network for Corrosion and Protection (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan 528399, China.
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20
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Crémet L, Leroy AG, Muller D, Delanou S, Burghelea A, Broquet A, Roquilly A, Caroff N. Antibiotic resistance heterogeneity and LasR diversity within Pseudomonas aeruginosa populations from pneumonia in intensive care unit patients. Int J Antimicrob Agents 2021; 57:106341. [PMID: 33857540 DOI: 10.1016/j.ijantimicag.2021.106341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/22/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022]
Abstract
This study investigated within-host heterogeneity of 66 Pseudomonas aeruginosa populations from pneumonia in 51 critically ill ventilated patients by examining 30 colonies per bronchoalveolar lavage (BAL). Differences in antibiotic susceptibility and quorum-sensing (QS) phenotypes were observed between the members of 14 (21.2%) and 10 (15.2%) populations, respectively. A significant association was found between QS deficiency and ceftazidime resistance. QS deficiency was associated with various lasR modifications, and was observed in 25 of 51 (49.0%) patients, including seven patients who received ≤48 h of ventilation. This study confirms the need to examine diverse colonies when analysing BAL cultures, particularly in β-lactam-exposed patients, to avoid missing ceftazidime- or imipenem-resistant isolates.
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Affiliation(s)
- Lise Crémet
- Laboratoire UPRES EA3826, IRS2 - Nantes Biotech, Université de Nantes, Nantes, France; Service de Bactériologie-Hygiène, Pôle de Biologie, CHU de Nantes, Nantes, France.
| | - Anne-Gaëlle Leroy
- Laboratoire UPRES EA3826, IRS2 - Nantes Biotech, Université de Nantes, Nantes, France; Service de Bactériologie-Hygiène, Pôle de Biologie, CHU de Nantes, Nantes, France
| | - Damien Muller
- Laboratoire UPRES EA3826, IRS2 - Nantes Biotech, Université de Nantes, Nantes, France; Service d'Anesthésie Réanimation Chirurgicale, Pôle d'Anesthésie-Réanimation, CHU de Nantes, Nantes, France
| | - Sandie Delanou
- Laboratoire UPRES EA3826, IRS2 - Nantes Biotech, Université de Nantes, Nantes, France
| | - Alexandra Burghelea
- Laboratoire UPRES EA3826, IRS2 - Nantes Biotech, Université de Nantes, Nantes, France
| | - Alexis Broquet
- Laboratoire UPRES EA3826, IRS2 - Nantes Biotech, Université de Nantes, Nantes, France
| | - Antoine Roquilly
- Laboratoire UPRES EA3826, IRS2 - Nantes Biotech, Université de Nantes, Nantes, France; Service d'Anesthésie Réanimation Chirurgicale, Pôle d'Anesthésie-Réanimation, CHU de Nantes, Nantes, France
| | - Nathalie Caroff
- Laboratoire UPRES EA3826, IRS2 - Nantes Biotech, Université de Nantes, Nantes, France
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Manson DE, O’Reilly MC, Nyffeler KE, Blackwell HE. Design, Synthesis, and Biochemical Characterization of Non-Native Antagonists of the Pseudomonas aeruginosa Quorum Sensing Receptor LasR with Nanomolar IC 50 Values. ACS Infect Dis 2020; 6:649-661. [PMID: 32037806 DOI: 10.1021/acsinfecdis.9b00518] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Quorum sensing (QS), a bacterial cell-to-cell communication system mediated by small molecules and peptides, has received significant interest as a potential target to block infection. The common pathogen Pseudomonas aeruginosa uses QS to regulate many of its virulence phenotypes at high cell densities, and the LasR QS receptor plays a critical role in this process. Small molecule tools that inhibit LasR activity would serve to illuminate its role in P. aeruginosa virulence, but we currently lack highly potent and selective LasR antagonists, despite considerable research in this area. V-06-018, an abiotic small molecule discovered in a high-throughput screen, represents one of the most potent known LasR antagonists but has seen little study since its initial report. Herein, we report a systematic study of the structure-activity relationships (SARs) that govern LasR antagonism by V-06-018. We synthesized a focused library of V-06-018 derivatives and evaluated the library for bioactivity using a variety of cell-based LasR reporter systems. The SAR trends revealed by these experiments allowed us to design probes with 10-fold greater potency than that of V-06-018 and 100-fold greater potency than other commonly used N-acyl-l-homoserine lactone (AHL)-based LasR antagonists, along with high selectivities for LasR. Biochemical experiments to probe the mechanism of antagonism by V-06-018 and its analogues support these compounds interacting with the native ligand-binding site in LasR and, at least in part, stabilizing an inactive form of the protein. The compounds described herein are the most potent and efficacious antagonists of LasR known and represent robust probes both for characterizing the mechanisms of LuxR-type QS and for chemical biology research in general in the growing QS field.
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Affiliation(s)
- Daniel E. Manson
- Department of Chemistry, University of Wisconsin−Madison, 110 University Ave., Madison, Wisconsin 53706 United States
| | - Matthew C. O’Reilly
- Department of Chemistry, University of Wisconsin−Madison, 110 University Ave., Madison, Wisconsin 53706 United States
| | - Kayleigh E. Nyffeler
- Department of Chemistry, University of Wisconsin−Madison, 110 University Ave., Madison, Wisconsin 53706 United States
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin−Madison, 110 University Ave., Madison, Wisconsin 53706 United States
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22
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Zhong L, Ravichandran V, Zhang N, Wang H, Bian X, Zhang Y, Li A. Attenuation of Pseudomonas aeruginosa Quorum Sensing by Natural Products: Virtual Screening, Evaluation and Biomolecular Interactions. Int J Mol Sci 2020; 21:E2190. [PMID: 32235775 PMCID: PMC7140002 DOI: 10.3390/ijms21062190] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
Natural products play vital roles against infectious diseases since ancient times and most drugs in use today are derived from natural sources. Worldwide, multi-drug resistance becomes a massive threat to the society with increasing mortality. Hence, it is very crucial to identify alternate strategies to control these 'super bugs'. Pseudomonas aeruginosa is an opportunistic pathogen reported to be resistant to a large number of critically important antibiotics. Quorum sensing (QS) is a cell-cell communication mechanism, regulates the biofilm formation and virulence factors that endow pathogenesis in various bacteria including P. aeruginosa. In this study, we identified and evaluated quorum sensing inhibitors (QSIs) from plant-based natural products against P. aeruginosa. In silico studies revealed that catechin-7-xyloside (C7X), sappanol and butein were capable of interacting with LasR, a LuxR-type quorum sensing regulator of P. aeruginosa. In vitro assays suggested that these QSIs significantly reduced the biofilm formation, pyocyanin, elastase, and rhamnolipid without influencing the growth. Especially, butein reduced the biofilm formation up to 72.45% at 100 µM concentration while C7X and sappanol inhibited the biofilm up to 66% and 54.26% respectively. Microscale thermophoresis analysis revealed that C7X had potential interaction with LasR (KD = 933±369 nM) and thermal shift assay further confirmed the biomolecular interactions. These results suggested that QSIs are able to substantially obstruct the P. aeruginosa QS. Since LuxR-type transcriptional regulator homologues are present in numerous bacterial species, these QSIs may be developed as broad spectrum anti-infectives in the future.
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Affiliation(s)
- Lin Zhong
- Helmholtz International Laboratory for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Vinothkannan Ravichandran
- Helmholtz International Laboratory for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Na Zhang
- Helmholtz International Laboratory for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hailong Wang
- Helmholtz International Laboratory for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaoying Bian
- Helmholtz International Laboratory for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz International Laboratory for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Aiying Li
- Helmholtz International Laboratory for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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McCready AR, Paczkowski JE, Cong JP, Bassler BL. An autoinducer-independent RhlR quorum-sensing receptor enables analysis of RhlR regulation. PLoS Pathog 2019; 15:e1007820. [PMID: 31194839 PMCID: PMC6564026 DOI: 10.1371/journal.ppat.1007820] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/07/2019] [Indexed: 01/03/2023] Open
Abstract
Quorum sensing is a chemical communication process that bacteria use to coordinate group behaviors. Pseudomonas aeruginosa, an opportunistic pathogen, employs multiple quorum-sensing systems to control behaviors including virulence factor production and biofilm formation. One P. aeruginosa quorum-sensing receptor, called RhlR, binds the cognate autoinducer N-butryl-homoserine lactone (C4HSL), and the RhlR:C4HSL complex activates transcription of target quorum-sensing genes. Here, we use a genetic screen to identify RhlR mutants that function independently of the autoinducer. The RhlR Y64F W68F V133F triple mutant, which we call RhlR*, exhibits ligand-independent activity in vitro and in vivo. RhlR* can drive wildtype biofilm formation and infection in a nematode animal model. The ability of RhlR* to properly regulate quorum-sensing-controlled genes in vivo depends on the quorum-sensing regulator RsaL keeping RhlR* activity in check. RhlR is known to function together with PqsE to control production of the virulence factor called pyocyanin. Likewise, RhlR* requires PqsE for pyocyanin production in planktonic cultures, however, PqsE is dispensable for RhlR*-driven pyocyanin production on surfaces. Finally, wildtype RhlR protein is not sufficiently stabilized by C4HSL to allow purification. However, wildtype RhlR can be stabilized by the synthetic ligand mBTL (meta-bromo-thiolactone) and RhlR* is stable without a ligand. These features enabled purification of the RhlR:mBTL complex and of RhlR* for in vitro examination of their biochemical activities. To our knowledge, this work reports the first RhlR protein purification.
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Affiliation(s)
- Amelia R. McCready
- The Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jon E. Paczkowski
- The Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jian-Ping Cong
- The Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Bonnie L. Bassler
- The Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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Shah MD, Kharkar PS, Sahu NU, Peerzada Z, Desai KB. Potassium 2-methoxy-4-vinylphenolate: a novel hit exhibiting quorum-sensing inhibition in Pseudomonas aeruginosa viaLasIR/RhlIR circuitry. RSC Adv 2019; 9:40228-40239. [PMID: 35542690 PMCID: PMC9076179 DOI: 10.1039/c9ra06612h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/18/2019] [Accepted: 11/19/2019] [Indexed: 02/05/2023] Open
Abstract
Effect of potassium 2-methoxy-4-vinylphenolate on quorum sensing inPseudomonas aeruginosa.
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Affiliation(s)
- Mayank D. Shah
- Sunandan Divatia School of Science
- SVKM's NMIMS (Deemed to be University)
- Mumbai
- India
| | - Prashant S. Kharkar
- Institute of Chemical Technology
- Category I Deemed to be University (MHRD/UGC)
- Mumbai-400019
- India
| | - Niteshkumar U. Sahu
- Institute of Chemical Technology
- Category I Deemed to be University (MHRD/UGC)
- Mumbai-400019
- India
| | - Zoya Peerzada
- Sunandan Divatia School of Science
- SVKM's NMIMS (Deemed to be University)
- Mumbai
- India
| | - Krutika B. Desai
- Mithibai College of Arts & Science & Amrutben Jivanlal College of Commerce & Economics
- Mumbai
- India
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