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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):e101840Plos

Abstract

Pseudomonas aeruginosa and Escherichia coli are resistant to wide range of antibiotics rendering the treatment of infections very difficult. A main mechanism attributed to the resistance is the function of efflux pumps. MexAB-OprM and AcrAB-TolC are the tripartite efflux pump assemblies, responsible for multidrug resistance in P. aeruginosa and E. coli respectively. Substrates that are more susceptible for efflux are predicted to have a common pharmacophore feature map. In this study, a new criterion of excluding compounds with efflux substrate-like features was used, thereby refining the selection process and enriching the inhibitor identification process. An in-house database of phytochemicals was created and screened using high-throughput virtual screening against AcrB and MexB proteins and filtered by matching with the common pharmacophore models (AADHR, ADHNR, AAHNR, AADHN, AADNR, AAADN, AAADR, AAANR, AAAHN, AAADD and AAADH) generated using known efflux substrates. Phytochemical hits that matched with any one or more of the efflux substrate models were excluded from the study. Hits that do not have features similar to the efflux substrate models were docked using XP docking against the AcrB and MexB proteins. The best hits of the XP docking were validated by checkerboard synergy assay and ethidium bromide accumulation assay for their efflux inhibition potency. Lanatoside C and diadzein were filtered based on the synergistic potential and validated for their efflux inhibition potency using ethidium bromide accumulation study. These compounds exhibited the ability to increase the accumulation of ethidium bromide inside the bacterial cell as evidenced by these increase in fluorescence in the presence of the compounds. With this good correlation between in silico screening and positive efflux inhibitory activity in vitro, the two compounds, lanatoside C and diadzein could be promising efflux pump inhibitors and effective to use in combination therapy against drug resistant strains of P. aeruginosa and E. coli.

Authors+Show Affiliations

Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, Tamilnadu, India.Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, Tamilnadu, India.Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, Tamilnadu, India.Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamilnadu, India.Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, Tamilnadu, India.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25025665

Citation

Aparna, Vasudevan, et al. "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, vol. 9, no. 7, 2014, pp. e101840.
Aparna V, Dineshkumar K, Mohanalakshmi N, et al. 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.
Aparna, V., Dineshkumar, K., Mohanalakshmi, N., Velmurugan, D., & Hopper, W. (2014). 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, 9(7), pp. e101840. doi:10.1371/journal.pone.0101840.
Aparna V, et al. 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. PubMed PMID: 25025665.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Aparna,Vasudevan, AU - Dineshkumar,Kesavan, AU - Mohanalakshmi,Narasumani, AU - Velmurugan,Devadasan, AU - Hopper,Waheeta, Y1 - 2014/07/15/ PY - 2014/03/29/received PY - 2014/06/12/accepted PY - 2014/7/16/entrez PY - 2014/7/16/pubmed PY - 2015/3/31/medline SP - e101840 EP - e101840 JF - PloS one JO - PLoS ONE VL - 9 IS - 7 N2 - Pseudomonas aeruginosa and Escherichia coli are resistant to wide range of antibiotics rendering the treatment of infections very difficult. A main mechanism attributed to the resistance is the function of efflux pumps. MexAB-OprM and AcrAB-TolC are the tripartite efflux pump assemblies, responsible for multidrug resistance in P. aeruginosa and E. coli respectively. Substrates that are more susceptible for efflux are predicted to have a common pharmacophore feature map. In this study, a new criterion of excluding compounds with efflux substrate-like features was used, thereby refining the selection process and enriching the inhibitor identification process. An in-house database of phytochemicals was created and screened using high-throughput virtual screening against AcrB and MexB proteins and filtered by matching with the common pharmacophore models (AADHR, ADHNR, AAHNR, AADHN, AADNR, AAADN, AAADR, AAANR, AAAHN, AAADD and AAADH) generated using known efflux substrates. Phytochemical hits that matched with any one or more of the efflux substrate models were excluded from the study. Hits that do not have features similar to the efflux substrate models were docked using XP docking against the AcrB and MexB proteins. The best hits of the XP docking were validated by checkerboard synergy assay and ethidium bromide accumulation assay for their efflux inhibition potency. Lanatoside C and diadzein were filtered based on the synergistic potential and validated for their efflux inhibition potency using ethidium bromide accumulation study. These compounds exhibited the ability to increase the accumulation of ethidium bromide inside the bacterial cell as evidenced by these increase in fluorescence in the presence of the compounds. With this good correlation between in silico screening and positive efflux inhibitory activity in vitro, the two compounds, lanatoside C and diadzein could be promising efflux pump inhibitors and effective to use in combination therapy against drug resistant strains of P. aeruginosa and E. coli. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/25025665/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_ L2 - http://dx.plos.org/10.1371/journal.pone.0101840 DB - PRIME DP - Unbound Medicine ER -