Green Synthesis of Yttrium Derivatives Nanoparticles Using Pine Needle Leaf Extract: Characterization, Docking, Antibacterial, and Antioxidant Potencies
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparation of the PNLE and Synthesis of the YNPs
2.2. Characterization Techniques of the YNPs
2.2.1. X-ray Diffraction (XRD)
2.2.2. Scanning Electron Microscopy (SEM) and Energy-Dispersive X-ray (EDX)
2.2.3. Transmission Electron Microscopy (TEM)
2.2.4. X-ray Photoelectron Spectroscopy (XPS)
2.2.5. Fourier Transform Infrared Spectroscopy (FTIR)
2.2.6. UV–Visible Spectroscopy (UV–Vis)
2.2.7. Photoluminescence (PL)
2.2.8. Vibrating Sample Magnetometry (VSM)
2.3. Antibacterial Activity of the YNPs
2.3.1. Preparation of the Bacterial Isolates
2.3.2. Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) Broth Microdilution Assay
2.3.3. Agar Well Diffusion Assay
2.3.4. Anti-Biofilm Assay
2.4. 1,1, Diphenyl 1-2 Picrylhydrazyl (DPPH) Free Radical Scavenging Assay
2.5. Molecular Docking Simulation
2.6. Statistical Analysis
3. Results
3.1. Characterization of the YNPs
3.1.1. X-ray Diffraction (XRD)
3.1.2. Transmission Electron Microscopic (TEM) Analysis
3.1.3. X-ray Photoelectron Spectroscopy (XPS)
3.1.4. Scanning Electron Microscopy (SEM) with Energy-Dispersive X-ray (EDX) Spectroscopy Analysis
3.1.5. Fourier Transform Infrared (FTIR) Analysis
3.1.6. Visual Observation and UV–Vis Spectroscopy Analysis
3.1.7. Photoluminescence (PL) Studies
3.1.8. Vibrating Sample Magnetometer (VSM)
3.2. Antibacterial Activity of the YNPs
3.2.1. Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) of the YNPs against the Bacterial Isolates
3.2.2. Agar Well Diffusion Results of the Yttrium Nanoparticles against the Bacterial Isolates
3.2.3. Inhibition of Bacterial Biofilm Formation and Destruction of Pre-Formed Bacterial Biofilms by the YNPs
3.3. Antioxidant Radical Scavenging Activity Results of the YNPs against DPPH
3.4. Molecular Docking of the YNPs with Antibacterial Target Proteins
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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NPs 1 | Presented Elements | Atomic % |
---|---|---|
YNPs 2 | O-1s | 71.44 |
Y–3d | 7.41 | |
N-1s | 13.4 | |
P-2p | 7.75 |
Sample | M20kOe (emu/g) 2 | Ms (emu/g) 3 | Mr × 10−3 (emu/g) 4 | Hci (Oe) 5 | S 6 |
---|---|---|---|---|---|
YNPs 1 | 0.664 | 0.681 | 85.540 | 289.24 | 0.127 |
Bacterial Isolates | Concentration (mg/mL) | |
---|---|---|
MIC 1 | MBC 2 | |
Gram-positive bacteria | ||
S. aureus | 1 | - 3 |
S. haemolyticus | 0.5 | - |
E. faecalis | 0.5 | - |
Gram-negative bacteria | ||
E. coli | 1 | - |
K. pneumonia | 0.5 | - |
P. aeruginosa | 0.5 | - |
YNPs Concentration (mg/mL) | Bacterial Isolates | |||||
---|---|---|---|---|---|---|
Gram-Positive | Gram-Negative | |||||
S. aureus | S. haemolyticus | E. faecalis | E. coli | K. pneumonia | P. aeruginosa | |
ZOI ± SEM (mm)2 | ||||||
0.0625 p-value Significance | 7.00 ± 0.00 0.001 *** | 7.00 ± 0.00 0.001 *** | 7.33 ± 0.27 ˂0.001 *** | 0.00 ± 0.00 ˂0.001 *** | 0.00 ± 0.00 ˂0.001 *** | 0.00 ± 0.00 ˂0.001 *** |
0.125 p-value Significance | 7.00 ± 0.00 0.001 *** | 7.00 ± 0.00 0.001 *** | 9.33 ± 0.27 0.001 *** | 0.0 ± 0.00 ˂0.001 *** | 0.0 ± 0.00 ˂0.001 *** | 0.00 ± 0.00 ˂0.001 *** |
0.25 p-value Significance | 7.33 ± 0.27 ˂0.001 *** | 7.33 ± 0.27 ˂0.001 *** | 9.33 ± 0.27 ˂0.001 *** | 0.00 ± 0.00 ˂0.001 *** | 0.0 ± 0.00 ˂0.001 *** | 0.00 ± 0.00 ˂0.001 *** |
0.5 p-value Significance | 7.33 ± 0.27 ˂0.001 *** | 7.33 ± 0.27 ˂0.001 *** | 10.00 ± 0.00 ˂0.001 *** | 7.33 ± 0.27 ˂0.001 *** | 7.33 ± 0.27 ˂0.001 *** | 7.33 ± 0.27 ˂0.001 *** |
1 p-value Significance | 8.33 ± 0.7 ˂0.001 *** | 7.33 ± 0.27 ˂0.002 ** | 10.00 ± 0.00 ˂0.001 *** | 10.33 ± 0.27 ˂0.001 *** | 7.33 ± 0.27 ˂0.001 *** | 7.33 ± 0.27 ˂0.001 *** |
Bacteria | Proteins 3D Structure | Hydrophilic Interactions | Hydrophobic Contacts | No. of H-Bonds | No. of Total Bonds | Affinity kcal mol-1 | |||
---|---|---|---|---|---|---|---|---|---|
Residue (H-Bond) | Length | Residue (Bond Type) | Length | ||||||
1 | E. coli | Asn46 (H-Bond) Val120 (H-Bond) Ser121 (H-Bond) Glu42(H-Bond) Asn46(H-Bond) Asn46(H-Bond) Gly119(H-Bond) | 2.31 2.10 2.73 3.17 2.72 2.64 2.54 | Gly119 (C–H Bond) Asn46 (Metal–Acceptor) | 2.54 2.88 | 7 | 9 | –12.54 | |
2 | E. faecalis | Ser367 (H-Bond) Thr418 (H-Bond) Tyr420 (H-Bond) Ile550(H-Bond) Gln552(H-Bond) Met654(H-Bond) Ile547(H-Bond) Phe416(H-Bond) | 2.11 2.95 3.03 3.66 2.23 2.85 2.54 2.14 | Phe416 (C–H Bond) Tyr420 (Pi–Donor H Bond) | 2.56 3.51 | 8 | 10 | –8.90 | |
3 | K. pneumonia | Ser71 (H-Bond) Arg161 (H-Bond) Ser181 (H-Bond) Ser182(H-Bond) Val186(H-Bond) Tyr247(H-Bond) Tyr264(H-Bond) Thr180(H-Bond) Pro67(H-Bond) Phe66(H-Bond) | 1.94 2.86 2.98 2.68 2.85 3.06 2.41 3.23 2.90 3.25 | Leu68 (C–H Bond) Phe72 (C–H Bond) Val186 (C–H Bond) Tyr247 (Metal–Acceptor) Tyr264 (Metal–Acceptor) | 2.66 2.71 3.40 3.29 3.09 | 10 | 15 | –10.22 | |
4 | P. aeruginosa | Gly38, (H-Bond) Arg61, (H-Bond) Ala127, (H-Bond) Asp73, (H-Bond) Tyr47, (H-Bond) Tyr64, (H-Bond) | 2.37 2.59 2.41 3.07 2.47 2.51 | Tyr64, (Pi–Lone Pair) Tyr47 (Pi–Donor Hydrogen) | 4.07 2.51 | 6 | 8 | –8.90 | |
5 | S. aureus | Asn11, (H-Bond) Arg52, (H-Bond) Lys203, (H-Bond) Gln105, (H-Bond) Arg239, (H-Bond) | 2.68 1.75 2.84 2.95 1.80 | - | - | 5 | 5 | –6.87 | |
6 | S. haemolyticus | Arg78, (H-Bond) His92, (H-Bond) Asp48, (H-Bond) Phe140, (H-Bond) Asp28, (H-Bond) Gly29, (H-Bond) | 2.17 2.08 2.65 2.93 2.93 2.35 | Gly29, (C–H bond) His92, (C–H bond) | 3.56 3.05 | 6 | 8 | –9.44 |
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Darwich, N.A.; Mezher, M.; Abdallah, A.M.; El-Sayed, A.F.; El Hajj, R.; Hamdalla, T.A.; Khalil, M.I. Green Synthesis of Yttrium Derivatives Nanoparticles Using Pine Needle Leaf Extract: Characterization, Docking, Antibacterial, and Antioxidant Potencies. Processes 2024, 12, 1713. https://doi.org/10.3390/pr12081713
Darwich NA, Mezher M, Abdallah AM, El-Sayed AF, El Hajj R, Hamdalla TA, Khalil MI. Green Synthesis of Yttrium Derivatives Nanoparticles Using Pine Needle Leaf Extract: Characterization, Docking, Antibacterial, and Antioxidant Potencies. Processes. 2024; 12(8):1713. https://doi.org/10.3390/pr12081713
Chicago/Turabian StyleDarwich, Nourhane A., Malak Mezher, Alaa M. Abdallah, Ahmed F. El-Sayed, Rana El Hajj, Taymour A. Hamdalla, and Mahmoud I. Khalil. 2024. "Green Synthesis of Yttrium Derivatives Nanoparticles Using Pine Needle Leaf Extract: Characterization, Docking, Antibacterial, and Antioxidant Potencies" Processes 12, no. 8: 1713. https://doi.org/10.3390/pr12081713