Discovery of AI-2 Quorum Sensing Inhibitors Targeting the LsrK/HPr Protein–Protein Interaction Site by Molecular Dynamics Simulation, Virtual Screening, and Bioassay Evaluation
Abstract
:1. Introduction
2. Results and Discussion
2.1. Analysis of the LsrK-HPr PPI Site
2.2. Virtual Screening Workflow (VSW)
2.3. LsrK Inhibition Assay
2.4. Cell-Based AI-2-Mediated QS Interference Assay
2.5. SPR Assay
2.6. Exploration of Structure-Activity Relationships (SARs)
3. Materials and Methods
3.1. MD Simulation, Virtual Screening and Pharmacophore Hypothesis Generation
3.1.1. Protein Preparation and Binding Site Detection
3.1.2. Molecular Dynamics (MD) Simulation
3.1.3. Estimation and Decomposition of the Binding Free Energy by gmx_MMPBSA
3.1.4. Virtual Screening
3.1.5. Pharmacophore Hypothesis Generation
3.2. Bioassay Methods
3.2.1. Overexpression and Purification of LsrK, LsrK-N, and HPr
3.2.2. LsrK Inhibition Assay
3.2.3. SPR Assay
3.2.4. Cell-Based AI-2-Mediated QS Interference Assay
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Compound ID | LsrK Inhibition (%) | LsrK (IC50) A | WHQ02 (IC50) B | WHQ01 (IC50) C |
---|---|---|---|---|
4171-0375 | 98 ± 7 | 26.13 ± 2.94 | 30.13 ± 1.62 * | 42.93 ± 1.63 * |
4929-0003 | 78 ± 12 | 80.75 ± 4.30 | 35.40 ± 2.29 * | 20.89 ± 1.24 * |
K659-0421 | 75 ± 8 | 73.69 ± 5.33 | 16.98 ± 0.37 * | 7.97 ± 0.38 * |
8020-4294 | 65 ± 9 | 148.40 ± 6.92 | 67.25 ± 4.32 | 24.86 ± 1.10 |
3229-1889 | 63 ± 4 | 121.31 ± 5.37 | 14.99 ± 1.24 | 24.72 ± 1.42 |
8012-5390 | 60 ± 4 | 147.13 ± 5.58 | 17.68 ± 0.98 | 23.28 ± 1.05 |
G268-0878 | 58 ± 5 | 128.73 ± 6.14 | 42.30 ± 1.42 | 30.55 ± 1.26 |
D715-0257 | 57 ± 7 | 152.57 ± 5.43 | 22.34 ± 2.15 | 21.10 ± 1.18 |
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Xu, Y.; Zeng, C.; Wen, H.; Shi, Q.; Zhao, X.; Meng, Q.; Li, X.; Xiao, J. Discovery of AI-2 Quorum Sensing Inhibitors Targeting the LsrK/HPr Protein–Protein Interaction Site by Molecular Dynamics Simulation, Virtual Screening, and Bioassay Evaluation. Pharmaceuticals 2023, 16, 737. https://doi.org/10.3390/ph16050737
Xu Y, Zeng C, Wen H, Shi Q, Zhao X, Meng Q, Li X, Xiao J. Discovery of AI-2 Quorum Sensing Inhibitors Targeting the LsrK/HPr Protein–Protein Interaction Site by Molecular Dynamics Simulation, Virtual Screening, and Bioassay Evaluation. Pharmaceuticals. 2023; 16(5):737. https://doi.org/10.3390/ph16050737
Chicago/Turabian StyleXu, Yijie, Chunlan Zeng, Huiqi Wen, Qianqian Shi, Xu Zhao, Qingbin Meng, Xingzhou Li, and Junhai Xiao. 2023. "Discovery of AI-2 Quorum Sensing Inhibitors Targeting the LsrK/HPr Protein–Protein Interaction Site by Molecular Dynamics Simulation, Virtual Screening, and Bioassay Evaluation" Pharmaceuticals 16, no. 5: 737. https://doi.org/10.3390/ph16050737