Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach
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Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
2
Department of Pharmaceutical Sciences, “Department of excellence 2018-2022”, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(16), 4041; https://doi.org/10.3390/ijms20164041
Received: 17 July 2019
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Revised: 9 August 2019
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Accepted: 15 August 2019
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Published: 19 August 2019
(This article belongs to the Special Issue Computer Simulation on Membrane Receptors)
The use and misuse of antibiotics has resulted in critical conditions for drug-resistant bacteria emergency, accelerating the development of antimicrobial resistance (AMR). In this context, the co-administration of an antibiotic with a compound able to restore sufficient antibacterial activity may be a successful strategy. In particular, the identification of efflux pump inhibitors (EPIs) holds promise for new antibiotic resistance breakers (ARBs). Indeed, bacterial efflux pumps have a key role in AMR development; for instance, NorA efflux pump contributes to Staphylococcus aureus (S. aureus) resistance against fluoroquinolone antibiotics (e.g., ciprofloxacin) by promoting their active extrusion from the cells. Even though NorA efflux pump is known to be a potential target for EPIs development, the absence of structural information about this protein and the little knowledge available on its mechanism of action have strongly hampered rational drug discovery efforts in this area. In the present work, we investigated at the molecular level the substrate recognition pathway of NorA through a Supervised Molecular Dynamics (SuMD) approach, using a NorA homology model. Specific amino acids were identified as playing a key role in the efflux pump-mediated extrusion of its substrate, paving the way for a deeper understanding of both the mechanisms of action and the inhibition of such efflux pumps.
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Keywords:
antimicrobial resistance; norA efflux pump; homology modeling; molecular dynamics simulation; supervised molecular dynamics
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Externally hosted supplementary file 1
Doi: 10.5281/zenodo.3370506
Link: https://zenodo.org/record/3370506#.XVmsx3vOP4d
Description: Title of Movie-S1 Movie-S1. MdfA-CLM recognition pathway. Legend of Movie-S1 The Movie is composed by four synchronized and animated panels that show different aspects of the SuMD simulation. The time evolution is reported in nanosecond. In the first panel (upper left), the molecular representation of the system is shown. The MdfA backbone is represented by the new cartoon style (cyan). The CLM is shown in yellow and by a transparent surface. The protein residues within 3 Å from the ligand are made explicit by a stick representation. In the second panel (upper-right), the CM-distance between the protein and the ligand centers of mass is reported. In the third panel (lower left), the MMGBSA energy profile is reported. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 MdfA residues most contacted by CLM during the whole simulation. Title of Movie-S2 Movie-S2. MdfA-CLM recognition pathway. Legend of Video-S2 The Movie shows the suMD trajectory of CLM on MdfA compared to the CLM crystallographic pose. MdfA is represented in cyan new cartoon transparency. The crystallographic pose is showed in yellow while the experimental one in light green. At 16.69 ns a RMSD value of 1.77 Å is highlighted. Title of Movie-S3 Movie-S3. NorA-CPX recognition pathway. Legend of Video-S3 The Movie is composed by four synchronized and animated panels that show different aspects of the SuMD simulation. The time evolution is reported in nanosecond. In the first panel (upper left), the system is shown. The NorA backbone is represented by the new cartoon style (red) and the protein residues within 3 Å of CPX are showed in stick. CPX is rendered by a green stick. In the second panel (upper-right), the distance between the centre of mass of the ligand and the protein during the trajectory is reported. In the third panel (lower left), the MMGBSA energy profile is reported. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 NorA residues most contacted by CPX during the whole suMD trajectory. It is important to note that the following video has a duration that is half of the simulation of suMD. However, this straid does not alter the description of the trajectory performed by the ligand. Title of Movie-S4 Movie-S2. Clustering of NorA-CPX recognition pathway. Legend of Video-S4 The Movie S4 depicts the clustering analysis of CPX during the whole suMD simulation. The NorA protein is shown in red new cartoon transparency. CPX is rendered by a light-green stick and by a transparent surface. The spheres are shown in 7 different colours, according to the different clusters. Each sphere dimension is in according to the cluster dimensions. After a first recognition site, the ligand conformations are clustered in different sites of the NorA channel. It is important to note that the following video has a duration that is half of the simulation of suMD. However, this straid does not alter the description of the trajectory performed by the ligand.
MDPI and ACS Style
Palazzotti, D.; Bissaro, M.; Bolcato, G.; Astolfi, A.; Felicetti, T.; Sabatini, S.; Sturlese, M.; Cecchetti, V.; Barreca, M.L.; Moro, S. Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach. Int. J. Mol. Sci. 2019, 20, 4041. https://doi.org/10.3390/ijms20164041
AMA Style
Palazzotti D, Bissaro M, Bolcato G, Astolfi A, Felicetti T, Sabatini S, Sturlese M, Cecchetti V, Barreca ML, Moro S. Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach. International Journal of Molecular Sciences. 2019; 20(16):4041. https://doi.org/10.3390/ijms20164041
Chicago/Turabian StylePalazzotti, Deborah, Maicol Bissaro, Giovanni Bolcato, Andrea Astolfi, Tommaso Felicetti, Stefano Sabatini, Mattia Sturlese, Violetta Cecchetti, Maria L. Barreca, and Stefano Moro. 2019. "Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach" International Journal of Molecular Sciences 20, no. 16: 4041. https://doi.org/10.3390/ijms20164041
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