Skip to content
2000
image of In silico Screening of Plant Compounds to Inhibit MexB Efflux Protein for the Enhancement of Meropenem Resistance against Pseudomonas aeruginosa MDR Infections

Abstract

Background

is a common cause of healthcare-associated infections such as Pneumonia, Bloodstream, Urinary tract, and Surgical site infections this bacterium is also reported to cause infections in cancerous cells. It is one of the most considered opportunistic human pathogens, especially in immunocompromised patients, and one of the top five pathogens of nosocomial diseases worldwide. Some are becoming more resistant to even antibiotics of last resort, including beta-lactams, fluoroquinolones, tetracycline, chloramphenicol, macrolides, and aminoglycosides, and are described as multidrug-resistant. Multiple lines of evidence suggest that the chief mechanism for resistance to antibiotics regulated by the efflux pumps. Antibiotic efflux pumps are membrane proteins that actively remove antibiotics from the bacterial cell, lowering on-target antibiotic concentrations to sub-toxic levels. The MexAB-OprM system is one of the largest multi-drug resistant clinically relevant efflux pumps with high expression levels in . Inhibition of these MDR efflux pumps can restore the activity of antimicrobial agents that are substrates for this protein. We performed molecular modelling studies in this study to discover novel Mex B efflux pump inhibitors. We evaluated the MIC of α-Bisabolol and Meropenem combination against Meropenem-resistant strains. This research opened up the possibility of using this plant compound α-Bisabolol and resistance drug Meropenem combination in the development of medicines for human consumption, possibly for the treatment of Hospital-Acquired Pneumonia, and multidrug-resisting infection caused by including wound and urinary infections which have been reported important HAI carbapenem class multidrug infections caused by the bacteria.

Method

The present study investigates the interactions of plant secondary metabolites Tables on Mex B efflux protein. It identifies lead molecules for developing adjuvants against efflux-mediated multidrug resistance in infections, enhances antibiotic activity against MDR pathogens, and evaluates the MIC value of the test plant compound (Bisabolol) and the resistant antibiotic (Meropenem).

Result

Among plant compounds, α-Bisabolol, myricetin, capsaicin, equenin, aloe-emodin, terpinene, fisetin, taxifolin, catechin, and galangin showed G-Scorehigher than -7 kcal/mol, and interact with active amino acids Mex B efflux protein which may affect the efflux transport of drug and enhance the antibiotic activity against MDR infection. According to docking experiments, α-bisabolol has a higher affinity energy to the MexB protein than Meropenem. Furthermore, α-bisabolol binds to the MexB binding site hydrophobic trap region of MexB, which may cause a conformational change in the transporter's pumping process, thereby affecting antibiotic efflux inhibition. The MICs against Meropenem were 12.5 µg/ml for antibiotic Meropenem and 6.24 μg/ml for the combination.

Conclusion

The study concluded that these plant secondary metabolite compounds could be used to develop adjuvant along with antibiotics to increase their activity against MexAB-OprM efflux-mediated multidrug-resisting infections. It was determined that α-bisabolol may have the potential to boost antibacterial activity when combined with antibiotics, as well as being a strong candidate for an efflux pump inhibitor. This is the first inclusion of the properties of a natural plant phytochemical, Bisabolol, utilized in combination with commercial resistant antibiotic Meropenem to enhance its activity against MDR pneumonia infection caused by .

Loading

Article metrics loading...

/content/journals/raaidd/10.2174/0127724344343717250404114236
2025-04-21
2025-08-13
Loading full text...

Full text loading...

References

  1. Compagne N Vieira Da Cruz A Müller RT Hartkoorn RC Flipo M Pos KM Update on the discovery of efflux pump inhibitors against critical priority gram-negative bacteria Antibiotics 2023 12 1 180 10.3390/antibiotics12010180
    [Google Scholar]
  2. Samreen F.A.Q. Qais F.A. Ahmad I. In silico screening and in vitro validation of phytocompounds as multidrug efflux pump inhibitor against E. coli. J. Biomol. Struct. Dyn. 2023 41 6 2189 2201 10.1080/07391102.2022.2029564 35067192
    [Google Scholar]
  3. Botelho J. Grosso F. Peixe L. Antibiotic resistance in Pseudomonas aeruginosa – Mechanisms, epidemiology and evolution. Drug Resist. Updat. 2019 44 100640 10.1016/j.drup.2019.07.002 31492517
    [Google Scholar]
  4. Tsutsumi K. Yonehara R. Ishizaka-Ikeda E. Miyazaki N. Maeda S. Iwasaki K. Nakagawa A. Yamashita E. Structures of the wild-type MexAB–OprM tripartite pump reveal its complex formation and drug efflux mechanism. Nat. Commun. 2019 10 1 1520 10.1038/s41467‑019‑09463‑9 30944318
    [Google Scholar]
  5. Behzadi P Ambrosi C Scribano D Editorial: Current perspectives on Pseudomonas aeruginosa: Epidemiology, virulence and contemporary strategies to combat multidrug-resistant (MDR) pathogens. Front. Microbiol. 2022 975616 10.3389/fmicb.2022.975616
    [Google Scholar]
  6. Alenazy R. Drug efflux pump inhibitors: A promising approach to counter multidrug resistance in gram-negative pathogens by targeting AcrB protein from AcrAB-TolC multidrug efflux Pump from Escherichia coli. Biology 2022 11 9 1328 10.3390/biology11091328
    [Google Scholar]
  7. Opperman TJ Nguyen ST Recent advances toward a molecular mechanism of efflux pump inhibition. Front. Microbiol. 2015 421 10.3389/fmicb.2015.00421
    [Google Scholar]
  8. Pan Y. Xu Y. Wang Z. Fang Y. Shen J. Overexpression of MexAB-OprM efflux pump in carbapenem-resistant Pseudomonas aeruginosa. Arch. Microbiol. 2016 198 6 565 571 10.1007/s00203‑016‑1215‑7 27060003
    [Google Scholar]
  9. Narita S. Tokuda H. Amino acids at positions 3 and 4 determine the membrane specificity of Pseudomonas aeruginosa lipoproteins. J. Biol. Chem. 2007 282 18 13372 13378 10.1074/jbc.M611839200 17350956
    [Google Scholar]
  10. Nanjan P. Bose V. Efflux-mediated multidrug resistance in critical gram-negative bacteria and natural efflux pump inhibitors. Curr. Drug Res. Rev. 2024 16 3 349 368 10.2174/0125899775271214240112071830 38288795
    [Google Scholar]
  11. Dias KJSO Miranda GM Bessa JR Terpenes as bacterial efflux pump inhibitors: A systematic review Front. Pharmacol. 2022 953982 10.3389/fphar.2022.953982
    [Google Scholar]
  12. Mahizan NA Yang SK Moo CL Terpene derivatives as a potential agent against antimicrobial resistance (AMR) pathogens. Molecules 2019 24 14 2631 10.3390/molecules24142631
    [Google Scholar]
  13. Seukep A.J. Kuete V. Nahar L. Sarker S.D. Guo M. Plant-derived secondary metabolites as the main source of efflux pump inhibitors and methods for identification. J. Pharm. Anal. 2020 10 4 277 290 10.1016/j.jpha.2019.11.002 32923005
    [Google Scholar]
  14. Collu F. Vargiu A.V. Dreier J. Cascella M. Ruggerone P. Recognition of imipenem and meropenem by the RND-transporter MexB studied by computer simulations. J. Am. Chem. Soc. 2012 134 46 19146 19158 10.1021/ja307803m 23146101
    [Google Scholar]
  15. Vargiu AV. Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump. Biochim. Biophys. Acta Gen. Subj. 2018 1862 4 836 845 10.1016/j.bbagen.2018.01.010
    [Google Scholar]
  16. Glavier M. Puvanendran D. Salvador D. Decossas M. Phan G. Garnier C. Frezza E. Cece Q. Schoehn G. Picard M. Taveau J.C. Daury L. Broutin I. Lambert O. Antibiotic export by MexB multidrug efflux transporter is allosterically controlled by a MexA-OprM chaperone-like complex. Nat. Commun. 2020 11 1 4948 10.1038/s41467‑020‑18770‑5 33009415
    [Google Scholar]
  17. Su C.C. Li M. Gu R. Takatsuka Y. McDermott G. Nikaido H. Yu E.W. Conformation of the AcrB multidrug efflux pump in mutants of the putative proton relay pathway. J. Bacteriol. 2006 188 20 7290 7296 10.1128/JB.00684‑06 17015668
    [Google Scholar]
  18. Alav I. Kobylka J. Kuth M.S. Pos K.M. Picard M. Blair J.M.A. Bavro V.N. Structure, assembly, and function of tripartite efflux and type 1 secretion systems in gram-negative bacteria. Chem. Rev. 2021 121 9 5479 5596 10.1021/acs.chemrev.1c00055 33909410
    [Google Scholar]
  19. Takatsuka Y. Chen C. Nikaido H. Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of Escherichia coli. Proc. Natl. Acad. Sci. USA 2010 107 15 6559 6565 10.1073/pnas.1001460107 20212112
    [Google Scholar]
  20. Aron Z. Opperman T.J. Optimization of a novel series of pyranopyridine RND efflux pump inhibitors. Curr. Opin. Microbiol. 2016 33 1 6 10.1016/j.mib.2016.05.007 27232955
    [Google Scholar]
  21. Aron Z. Opperman T.J. The hydrophobic trap—the Achilles heel of RND efflux pumps. Res. Microbiol. 2018 169 7-8 393 400 10.1016/j.resmic.2017.11.001 29146106
    [Google Scholar]
  22. Aparna V Dineshkumar K Mohanalakshmi N Velmurugan D Hopper W Identification of natural compound inhibitors for multidrug efflux pumps of Escherichia coli and Pseudomonas aeruginosa using in silico high-throughput virtual screening and in vitro validation. PLoS One 2014 9 7 e101840 10.1371/journal.pone.0101840
    [Google Scholar]
  23. Gervasoni S. Mehla J. Bergen C.R. Leus I.V. Margiotta E. Malloci G. Bosin A. Vargiu A.V. Lomovskaya O. Rybenkov V.V. Ruggerone P. Zgurskaya H.I. Molecular determinants of avoidance and inhibition of Pseudomonas aeruginosa MexB efflux pump. MBio 2023 14 4 e01403-23 10.1128/mbio.01403‑23 37493633
    [Google Scholar]
  24. Zgurskaya HI Bacterial efflux transporters' polyspecificity - A gift and a curse? Curr Opin Microbiol 2021 61 115 123 10.1016/j.mib.2021.03.009
    [Google Scholar]
  25. Athar M. Gervasoni S. Catte A. Basciu A. Malloci G. Ruggerone P. Vargiu A.V. Tripartite efflux pumps of the RND superfamily: What did we learn from computational studies? Microbiology 2023 169 3 001307 10.1099/mic.0.001307 36972322
    [Google Scholar]
  26. Ferrer-Espada R. Shahrour H. Pitts B. Stewart P.S. Sánchez-Gómez S. Martínez-de-Tejada G. A permeability-increasing drug synergizes with bacterial efflux pump inhibitors and restores susceptibility to antibiotics in multi-drug resistant Pseudomonas aeruginosa strains. Sci. Rep. 2019 9 1 3452 10.1038/s41598‑019‑39659‑4 30837499
    [Google Scholar]
  27. Avakh A. Grant G.D. Cheesman M.J. Kalkundri T. Hall S. The art of war with Pseudomonas aeruginosa: Targeting mex efflux pumps directly to strategically enhance antipseudomonal drug efficacy. Antibiotics 2023 12 8 1304 10.3390/antibiotics12081304 37627724
    [Google Scholar]
  28. Burley S.K. Bhikadiya C. Bi C. Bittrich S. Chen L. Crichlow G.V. Christie C.H. Dalenberg K. Di Costanzo L. Duarte J.M. Dutta S. Feng Z. Ganesan S. Goodsell D.S. Ghosh S. Green R.K. Guranović V. Guzenko D. Hudson B.P. Lawson C.L. Liang Y. Lowe R. Namkoong H. Peisach E. Persikova I. Randle C. Rose A. Rose Y. Sali A. Segura J. Sekharan M. Shao C. Tao Y.P. Voigt M. Westbrook J.D. Young J.Y. Zardecki C. Zhuravleva M. RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Res. 2021 49 D1 D437 D451 10.1093/nar/gkaa1038 33211854
    [Google Scholar]
  29. Bioinformatics X.X. Discovery D. Bioinformatics and drug discovery. Curr. Top. Med. Chem. 2017 17 15 1709 1726 10.2174/1568026617666161116143440 27848897
    [Google Scholar]
  30. Vijayakumar S. Manogar P. Prabhu S. Sanjeevkumar Singh R.A. Novel ligand-based docking; molecular dynamic simulations; and absorption, distribution, metabolism, and excretion approach to analyzing potential acetylcholinesterase inhibitors for Alzheimer’s disease. J. Pharm. Anal. 2018 8 6 413 420 10.1016/j.jpha.2017.07.006 30595949
    [Google Scholar]
  31. Sinha S. Patel S. Athar M. Vora J. Chhabria M.T. Jha P.C. Shrivastava N. Structure-based identification of novel sirtuin inhibitors against triple negative breast cancer: An in silico and in vitro study. Int. J. Biol. Macromol. 2019 140 454 468 10.1016/j.ijbiomac.2019.08.061 31404596
    [Google Scholar]
  32. Hashem H.E. In silico approach of some selected honey constituents as SARS-CoV-2 main protease (COVID-19) inhibitors. Eur. J. Med. Oncol. 2020 4 3 196 200 10.14744/ejmo.2020.36102
    [Google Scholar]
  33. Mohanty M. Mohanty P.S. Molecular docking in organic, inorganic, and hybrid systems: A tutorial review. Monatsh. Chem. 2023 154 7 683 707 10.1007/s00706‑023‑03076‑1 37361694
    [Google Scholar]
  34. Hatami S. Sirous H. Mahnam K. Najafipour A. Fassihi A. Preparing a database of corrected protein structures important in cell signaling pathways. Res. Pharm. Sci. 2023 18 1 67 78 10.4103/1735‑5362.363597 36846730
    [Google Scholar]
  35. Rolta R. Salaria D. Kumar V. Patel C.N. Sourirajan A. Baumler D.J. Dev K. Molecular docking studies of phytocompounds of Rheum emodi Wall with proteins responsible for antibiotic resistance in bacterial and fungal pathogens: In silico approach to enhance the bio-availability of antibiotics. J. Biomol. Struct. Dyn. 2022 40 8 3789 3803 10.1080/07391102.2020.1850364 33225862
    [Google Scholar]
  36. Nurhan A.D. Gani M.A. Maulana S. Siswodihardjo S. Ardianto C. Khotib J. Molecular docking studies for protein-targeted drug development in SARS-CoV-2. Lett. Drug Des. Discov. 2022 19 5 428 439 10.2174/1570180818666210512021619
    [Google Scholar]
  37. Shah B. Modi P. Sagar S.R. In silico studies on therapeutic agents for COVID-19: Drug repurposing approach. Life Sci. 2020 252 117652 10.1016/j.lfs.2020.117652 32278693
    [Google Scholar]
  38. Rolta R. Yadav R. Salaria D. Trivedi S. Imran M. Sourirajan A. Baumler D.J. Dev K. In silico screening of hundred phytocompounds of ten medicinal plants as potential inhibitors of nucleocapsid phosphoprotein of COVID-19: an approach to prevent virus assembly. J. Biomol. Struct. Dyn. 2021 39 18 7017 7034 10.1080/07391102.2020.1804457 32851912
    [Google Scholar]
  39. Yusof I. Segall M.D. Considering the impact drug-like properties have on the chance of success. Drug Discov. Today 2013 18 13-14 659 666 10.1016/j.drudis.2013.02.008 23458995
    [Google Scholar]
  40. Filimonov D.A. Lagunin A.A. Gloriozova T.A. Rudik A.V. Druzhilovskii D.S. Pogodin P.V. Poroikov V.V. Prediction of the biological activity spectra of organic compounds using the pass online web resource. Chem. Heterocycl. Compd. 2014 50 3 444 457 10.1007/s10593‑014‑1496‑1
    [Google Scholar]
  41. Amin M.R. Yasmin F. Hosen M.A. Dey S. Mahmud S. Saleh M.A. Emran T.B. Hasan I. Fujii Y. Yamada M. Ozeki Y. Kawsar S.M.A. Synthesis, antimicrobial, anticancer, PASS, molecular docking, molecular dynamic simulations & pharmacokinetic predictions of some Methyl β-D-Galactopyranoside analogs. Molecules 2021 26 22 7016 10.3390/molecules26227016 34834107
    [Google Scholar]
  42. Chugh A Sehgal I Khurana N Verma K Rolta R Vats P Salaria D Fadare OA Awofisayo O Verma A Phartyal R Verma M Comparative docking studies of drugs and phytocompounds for emerging variants of SARS-CoV-2 3 Biotech 2023 13 1 36 10.1007/s13205‑022‑03450‑6
    [Google Scholar]
  43. Mohs RC Greig NH Drug discovery and development: Role of basic biological research Alzheimers Demen 2017 3 4 651 657 10.1016/j.trci.2017.10.005
    [Google Scholar]
  44. Zhou Y. Hou Z. Fang C. Xue X. Da F. Wang Y. Bai H. Luo X. Comparison of microplate and macrodilution methods in time–kill study of new antimicrobial drugs. Folia Microbiol. 2013 58 1 9 16 10.1007/s12223‑012‑0168‑8 22684972
    [Google Scholar]
  45. Ahmed S. Shohael A.M. In-silico studies of four anthraquinones of Senna alata L. as potential antifungal compounds. Pharmacology 2019 2 259 268
    [Google Scholar]
/content/journals/raaidd/10.2174/0127724344343717250404114236
Loading
/content/journals/raaidd/10.2174/0127724344343717250404114236
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test