Identification of anti-pathogenic activity among in silico predicted small-molecule inhibitors of Pseudomonas aeruginosa LasR or nitric oxide reductase (NOR)
DOI:
https://doi.org/10.33393/dti.2023.2638Keywords:
Antimicrobial resistance (AMR), Nitric oxide, Nitrosative stress, Priority pathogen, Pseudomonas aeruginosa, Quorum sensing (QS), VirulenceAbstract
Introduction: Antibiotic-resistant Pseudomonas aeruginosa strains cause considerable morbidity and mortality globally. Identification of novel targets in this notorious pathogen is urgently warranted to facilitate discovery of new anti-pathogenic agents against it. This study attempted to identify small-molecule inhibitors of two important proteins LasR and nitric oxide reductase (NOR) in P. aeruginosa. ‘Las’ system can be said to be the ‘master’ regulator of quorum sensing in P. aeruginosa, whose receptor protein is LasR. Similarly, NOR is crucial to detoxification of reactive nitrogen species.
Methods: In silico identification of potential LasR or NOR inhibitors was attempted through a virtual screening platform AtomNet® to obtain a final subset of <100 top scoring compounds. These compounds were evaluated for their in vivo anti-pathogenic activity by challenging the model host Caenorhabditis elegans with P. aeruginosa in the presence or absence of test compounds. Survival of the worm population in 24-well assay plates was monitored over a period of 5 days microscopically.
Results: Of the 96 predicted LasR inhibitors, 11 exhibited anti-Pseudomonas activity (23%-96% inhibition of bacterial virulence as per third-day end-point) at 25-50 µg/mL. Of the 85 predicted NOR inhibitors, 8 exhibited anti-Pseudomonas activity (40%-85% inhibition of bacterial virulence as per second-day end-point) at 25-50 µg/mL.
Conclusion: Further investigation on molecular mode of action of compounds found active in this study is warranted. Virtual screening can be said to be a useful tool in narrowing down the list of compounds requiring actual wet-lab screening, saving considerable time and efforts for drug discovery.
Downloads
References
Murray CJ, Ikuta KS, Sharara F, et al; Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629-655. https://doi.org/10.1016/S0140-6736(21)02724-0 PMID:35065702 DOI: https://doi.org/10.1016/S0140-6736(21)02724-0
Tacconelli E, Carrara E, Savoldi A, et al; WHO Pathogens Priority List Working Group. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis. 2018;18(3):318-327. https://doi.org/10.1016/S1473-3099(17)30753-3 PMID:29276051 DOI: https://doi.org/10.1016/S1473-3099(17)30753-3
Singh SB, Barrett JF. Empirical antibacterial drug discovery – foundation in natural products. Biochem Pharmacol. 2006;71(7):1006-1015. https://doi.org/10.1016/j.bcp.2005.12.016 PMID:16412984 DOI: https://doi.org/10.1016/j.bcp.2005.12.016
Payne DJ, Gwynn MN, Holmes DJ, Pompliano DL. Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat Rev Drug Discov. 2007;6(1):29-40. https://doi.org/10.1038/nrd2201 PMID:17159923 DOI: https://doi.org/10.1038/nrd2201
Jaeger T, Flohé L. The thiol-based redox networks of pathogens: unexploited targets in the search for new drugs. Biofactors. 2006;27(1-4):109-120. https://doi.org/10.1002/biof.5520270110 PMID:17012768 DOI: https://doi.org/10.1002/biof.5520270110
Ruparel FJ, Shah SK, Patel JH, Thakkar NR, Gajera GN, Kothari VO. Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations. Drug Target Insights. 2023;17:58-69. https://doi.org/10.33393/dti.2023.2595 PMID:37275512 DOI: https://doi.org/10.33393/dti.2023.2595
Groleau MC, de Oliveira Pereira T, Dekimpe V, Déziel E. PqsE is essential for RhlR-dependent quorum sensing regulation in Pseudomonas aeruginosa. mSystems. 2020;5(3):10-128. https://doi.org/10.1128/mSystems.00194-20 PMID:32457239 DOI: https://doi.org/10.1128/mSystems.00194-20
Joshi C, Kothari V. Bacterial stress-response machinery as a target for next-generation antimicrobials. Infect Disord Drug Targets. 2022;22(6):e210322202493. https://doi.org/10.2174/1871526522666220321153332 PMID:35319398 DOI: https://doi.org/10.2174/1871526522666220321153332
Porcheron G, Dozois CM. Interplay between iron homeostasis and virulence: fur and RyhB as major regulators of bacterial pathogenicity. Vet Microbiol. 2015;179(1-2):2-14. https://doi.org/10.1016/j.vetmic.2015.03.024 PMID:25888312 DOI: https://doi.org/10.1016/j.vetmic.2015.03.024
Hofmann L, Hirsch M, Ruthstein S. Advances in understanding of the copper homeostasis in Pseudomonas aeruginosa. Int J Mol Sci. 2021;22(4):2050. https://doi.org/10.3390/ijms22042050 PMID:33669570 DOI: https://doi.org/10.3390/ijms22042050
Chen H, Han J, Wang L. Diels-Alder cycloadditions of N-arylpyrroles via aryne intermediates using diaryliodonium salts. Beilstein J Org Chem. 2018;14(1):354-363. https://doi.org/10.3762/bjoc.14.23 PMID:29507640 DOI: https://doi.org/10.3762/bjoc.14.23
Kamal AA, Maurer CK, Allegretta G, Haupenthal J, Empting M, Hartmann RW. Quorum sensing inhibitors as pathoblockers for Pseudomonas aeruginosa infections: a new concept in anti-infective drug discovery. Antibacterials. 2018;II:185-210. https://doi.org/10.1007/7355_2017_17 DOI: https://doi.org/10.1007/7355_2017_17
Bonvicini F, Mandrone M, Cosa S. Editorial: pathoblockers and antivirulence agents of plant-origin for the management of multidrug resistant pathogens. Front Microbiol. 2023;14:1201495. https://doi.org/10.3389/fmicb.2023.1201495 PMID:37180278 DOI: https://doi.org/10.3389/fmicb.2023.1201495
Huang Y, Chen Y, Zhang LH. The roles of microbial cell-cell chemical communication systems in the modulation of antimicrobial resistance. Antibiotics (Basel). 2020;9(11):779. https://doi.org/10.3390/antibiotics9110779 PMID:33171916 DOI: https://doi.org/10.3390/antibiotics9110779
Nandi S. Recent advances in ligand and structure based screening of potent quorum sensing inhibitors against antibiotic resistance induced bacterial virulence. Recent Pat Biotechnol. 2016;10(2):195-216. https://doi.org/10.2174/1872208310666160728104450 PMID:27468815 DOI: https://doi.org/10.2174/1872208310666160728104450
Kumar M, Saxena M, Saxena AK, Nandi S. Recent breakthroughs in various antimicrobial resistance induced quorum sensing biosynthetic pathway mediated targets and design of their inhibitors. Comb Chem High Throughput Screen. 2020;23(6):458-476. https://doi.org/10.2174/1386207323666200425205808 PMID:32334498 DOI: https://doi.org/10.2174/1386207323666200425205808
Abisado RG, Benomar S, Klaus JR, Dandekar AA, Chandler JR. Bacterial quorum sensing and microbial community interactions. MBio. 2018;9(3):10-128. https://doi.org/10.1128/mBio.02331-17 PMID:29789364 DOI: https://doi.org/10.1128/mBio.02331-17
Della Sala G, Teta R, Esposito G, Costantino V. The chemical language of gram-negative bacteria. InQuorum Sensing. Academic Press; 2019:3-28. https://doi.org/10.1016/B978-0-12-814905-8.00001-0. DOI: https://doi.org/10.1016/B978-0-12-814905-8.00001-0
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 Aug 10;10:1203672. https://doi.org/10.3389/fmolb.2023.1203672 PMID: 37635941 DOI: https://doi.org/10.3389/fmolb.2023.1203672
Kostylev M, Kim DY, Smalley NE, Salukhe I, Greenberg EP, Dandekar AA. Evolution of the Pseudomonas aeruginosa quorum-sensing hierarchy. Proc Natl Acad Sci USA. 2019;116(14):7027-7032. https://doi.org/10.1073/pnas.1819796116 PMID:30850547 DOI: https://doi.org/10.1073/pnas.1819796116
Schuster M, Urbanowski ML, Greenberg EP. Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR. Proc Natl Acad Sci USA. 2004;101(45):15833-15839. https://doi.org/10.1073/pnas.0407229101 PMID:15505212 DOI: https://doi.org/10.1073/pnas.0407229101
Maddocks SE. Novel targets of antimicrobial therapies. Microbiol Spectr. 2016;4(2):10-128. https://doi.org/10.1128/microbiolspec.VMBF-0018-2015 PMID:27227296 DOI: https://doi.org/10.1128/microbiolspec.VMBF-0018-2015
Haque S, Ahmad F, Dar SA, et al. Developments in strategies for Quorum Sensing virulence factor inhibition to combat bacterial drug resistance. Microb Pathog. 2018;121:293-302. https://doi.org/10.1016/j.micpath.2018.05.046 PMID:29857121 DOI: https://doi.org/10.1016/j.micpath.2018.05.046
Geske GD, O’Neill JC, Blackwell HE. Expanding dialogues: from natural autoinducers to non-natural analogues that modulate quorum sensing in Gram-negative bacteria. Chem Soc Rev. 2008;37(7):1432-1447. https://doi.org/10.1039/b703021p PMID:18568169 DOI: https://doi.org/10.1039/b703021p
Packiavathy IASV, Kannappan A, Thiyagarajan S, et al. AHL-Lactonase producing Psychrobacter sp. from Palk Bay sediment mitigates quorum sensing-mediated virulence production in Gram negative bacterial pathogens. Front Microbiol. 2021;12:634593. https://doi.org/10.3389/fmicb.2021.634593 PMID:33935995 DOI: https://doi.org/10.3389/fmicb.2021.634593
Poole K. Stress responses as determinants of antimicrobial resistance in Pseudomonas aeruginosa: multidrug efflux and more. Can J Microbiol. 2014;60(12):783-791. https://doi.org/10.1139/cjm-2014-0666 PMID:25388098 DOI: https://doi.org/10.1139/cjm-2014-0666
Joshi C, Patel P, Palep H, Kothari V. Validation of the anti-infective potential of a polyherbal ‘Panchvalkal’ preparation, and elucidation of the molecular basis underlining its efficacy against Pseudomonas aeruginosa. BMC Complement Altern Med. 2019;19(1):1-5. https://doi.org/10.1186/s12906-019-2428-5 PMID:30654785 DOI: https://doi.org/10.1186/s12906-019-2428-5
Van Alst NE, Picardo KF, Iglewski BH, Haidaris CG. Nitrate sensing and metabolism modulate motility, biofilm formation, and virulence in Pseudomonas aeruginosa. Infect Immun. 2007;75(8):3780-3790. https://doi.org/10.1128/IAI.00201-07 PMID:17526746 DOI: https://doi.org/10.1128/IAI.00201-07
Han S, Liu J, Li M, et al. DNA Methyltransferase regulates nitric oxide homeostasis and virulence in a chronically adapted Pseudomonas aeruginosa strain. mSystems. 2022;7(5):e0043422. https://doi.org/10.1128/msystems.00434-22 PMID:36106744 DOI: https://doi.org/10.1128/msystems.00434-22
Toyofuku M, Yoon SS. Nitric oxide, an old molecule with noble functions in Pseudomonas aeruginosa biology. Adv Microb Physiol. 2018;72:117-145. https://doi.org/10.1016/bs.ampbs.2018.01.005 PMID:29778213 DOI: https://doi.org/10.1016/bs.ampbs.2018.01.005
Barraud N, Kelso MJ, Rice SA, Kjelleberg S. Nitric oxide: a key mediator of biofilm dispersal with applications in infectious diseases. Curr Pharm Des. 2015;21(1):31-42. https://doi.org/10.2174/1381612820666140905112822 PMID:25189865 DOI: https://doi.org/10.2174/1381612820666140905112822
Carvalho SM, Beas JZ, Videira MAM, Saraiva LM. Defenses of multidrug resistant pathogens against reactive nitrogen species produced in infected hosts. Adv Microb Physiol. 2022;80:85-155. https://doi.org/10.1016/bs.ampbs.2022.02.001 PMID:35489794 DOI: https://doi.org/10.1016/bs.ampbs.2022.02.001
Wang Z, Xie X, Shang D, et al. A c-di-GMP signaling cascade controls motility, biofilm formation, and virulence in Burkholderia thailandensis. Appl Environ Microbiol. 2022;88(7):e0252921. https://doi.org/10.1128/aem.02529-21 PMID:35323023 DOI: https://doi.org/10.1128/aem.02529-21
Kakishima K, Shiratsuchi A, Taoka A, Nakanishi Y, Fukumori Y. Participation of nitric oxide reductase in survival of Pseudomonas aeruginosa in LPS-activated macrophages. Biochem Biophys Res Commun. 2007;355(2):587-591. https://doi.org/10.1016/j.bbrc.2007.02.017 PMID:17307144 DOI: https://doi.org/10.1016/j.bbrc.2007.02.017
Abelyan N, Grabski H, Tiratsuyan S. In silico screening of flavones and its derivatives as potential inhibitors of quorum-sensing regulator LasR of Pseudomonas aeruginosa. Mol Biol (Mosk). 2020;54(1):153-163. https://doi.org/10.1134/S0026893320010021 PMID:32163399 DOI: https://doi.org/10.1134/S0026893320010021
Narayanaswamy R, Prabhakaran VS, Al-Ansari MM, Al-Humaid LA, Tiwari P. An in silico analysis of synthetic and natural compounds as inhibitors of nitrous oxide reductase (N2OR) and nitrite reductase (NIR). Toxics. 2023;11(8):660. https://doi.org/10.3390/toxics11080660 PMID:37624165 DOI: https://doi.org/10.3390/toxics11080660
Wallach I, Dzamba M, Heifets A. AtomNet: a deep convolutional neural network for bioactivity prediction in structure-based drug discovery. arXiv preprint arXiv:1510.02855. 2015. https://doi.org/10.48550/arXiv.1510.02855
Patel P, Joshi C, Kothari V. Antipathogenic potential of a polyherbal wound-care formulation (herboheal) against certain wound-infective gram-negative bacteria. Adv Pharmacol Sci. 2019;2019:1739868. https://doi.org/10.1155/2019/1739868 PMID:30833966 DOI: https://doi.org/10.1155/2019/1739868
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. https://doi.org/10.1016/j.ejmech.2022.114629 PMID:35961070 DOI: https://doi.org/10.1016/j.ejmech.2022.114629
Hernando-Amado S, Alcalde-Rico M, Gil-Gil T, Valverde JR, Martínez JL. Naringenin inhibition of the Pseudomonas aeruginosa quorum sensing response is based on its time-dependent competition with N-(3-Oxo-dodecanoyl)-L-homoserine lactone for LasR binding. Front Mol Biosci. 2020;7:25. https://doi.org/10.3389/fmolb.2020.00025 PMID:32181260 DOI: https://doi.org/10.3389/fmolb.2020.00025
O’Brien KT, Noto JG, Nichols-O’Neill L, Perez LJ. Potent irreversible inhibitors of LasR quorum sensing in Pseudomonas aeruginosa. ACS Med Chem Lett. 2015;6(2):162-167. https://doi.org/10.1021/ml500459f PMID:25699144 DOI: https://doi.org/10.1021/ml500459f
Walsh C. Where will new antibiotics come from? Nat Rev Microbiol. 2003;1(1):65-70. https://doi.org/10.1038/nrmicro727 PMID:15040181 DOI: https://doi.org/10.1038/nrmicro727
Allen RC, Popat R, Diggle SP, Brown SP. Targeting virulence: can we make evolution-proof drugs? Nat Rev Microbiol. 2014;12(4):300-308. https://doi.org/10.1038/nrmicro3232 PMID:24625893 DOI: https://doi.org/10.1038/nrmicro3232
Additional Files
Published
How to Cite
Issue
Section
Categories
License
Copyright (c) 2023 The Authors
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Authors contributing to Drug Target Insights agree to publish their articles under the Creative Common Attribution Non Commercial 4.0 (CC-BY-NC 4.0) license, which allows third parties to re-use the work without permission as long as the work is properly referenced and the use is non-commercial.
Accepted 2023-09-04
Published 2023-09-28
