Limoniastrum monopetalum–Mediated Nanoparticles and Biomedicines: In Silico Study and Molecular Prediction of Biomolecules
Abstract
:1. Introduction
2. Results
2.1. Characterizations of the Prepared Nanoparticles
2.2. The Antibacterial Activity
2.3. Identification of the Chemical Components of the Extract
2.4. In Silico Study
2.4.1. Prediction of Antibacterial Activity
2.4.2. Molecular Target Predictions
2.4.3. Molecular Docking Study
2.4.4. Pharmacokinetic Parameters Evaluation
2.4.5. Toxicity Assessment
2.4.6. Prediction of Cardiac Toxicity
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Morphological Identification
4.2. Preparation of Limoniastrum Monopetalum Extract
4.3. Preparation of AgNPs
4.4. Characterization of L-AgNPs
4.5. Analysis of Surface Functional Groups
4.6. Antibacterial Screening
4.7. LC–QTOF–MS Analysis for Metabolites Detection
4.8. Antibacterial Activity Prediction
4.9. Target and Pharmacokinetic Prediction
4.10. Molecular Docking Study
4.11. Organ and Endpoint Toxicity Assessment
4.12. Cardiac Toxicity Prediction
4.13. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Biological Activities for Metabolites (Antibacterial) | Pa | Pi |
---|---|---|
1 | 0.333 | 0.048 |
2 | 0.388 | 0.033 |
3 | 0.320 | 0.053 |
4 | 0.274 | 0.070 |
5 | 0.349 | 0.043 |
6 | 0.421 | 0.025 |
7 | 0.395 | 0.031 |
8 | 0.569 | 0.011 |
9 | 0.359 | 0.041 |
10 | 0.375 | 0.037 |
11 | 0.537 | 0.013 |
12 | 0.677 | 0.005 |
Metabolite Number | Glide Docking Score | Molecular Interactions |
---|---|---|
1 | −4.65 | THR199 and zinc coordination |
2 | −4.97 | ASN67, THR200, PRO201, and zinc coordination |
3 | −5.347 | HIS94, THR200, and zinc coordination |
4 | −5.16 | ASN62, ASN67, THR199, and zinc coordination |
5 | −4.88 | THR200 and zinc coordination |
6 | −6.12 | GLU92, THR199, and zinc coordination |
7 | −5.85 | HIP64, THR199, and zinc coordination |
8 | −7.89 | ASN67, GLU69, THR199, and zinc coordination |
9 | −5.18 | ASN67, THR199, and zinc coordination |
10 | −4.64 | GLN92 |
11 | −6.40 | ASN67, GLU69, THR199, THR200, and zinc coordination |
12 | −10.37 | HIS94, THR199, HIP64, HIS4, TRP5, PRO201, and zinc coordination |
51J (Native ligand) | −9.580 | ASN67, GLN92, THR199, THR200, and zinc coordination |
Properties | Parameters | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Physicochemical Properties | MW (g/mol) | 194.18 | 330.46 | 290.27 | 358.39 | 184.15 | 318.24 | 302.24 | 492.43 | 224.21 | 316.26 | 354.31 | 610.52 |
HBA | 4 | 5 | 6 | 6 | 5 | 8 | 7 | 12 | 5 | 7 | 9 | 16 | |
HBD | 2 | 4 | 5 | 2 | 3 | 6 | 5 | 7 | 2 | 4 | 6 | 10 | |
Lipophilicity Log Po/w | iLOGP | 1.62 | 3.18 | 1.47 | 2.67 | 0.97 | 1.08 | 1.94 | 2.00 | 1.63 | 2.35 | 0.96 | 1.58 |
XLOGP3 | 1.51 | 3.15 | 0.36 | 2.28 | 0.86 | 1.18 | 2.17 | −0.39 | 1.46 | 1.87 | −0.42 | −0.33 | |
MLOGP | 1.00 | 2.01 | 0.24 | 1.17 | 0.18 | −1.08 | −0.56 | −2.43 | 0.73 | −0.31 | −1.05 | −3.89 | |
Absorption | Water solubility | Soluble | Soluble | Soluble | Moderately soluble | Soluble | Soluble | Soluble | Soluble | Soluble | Soluble | Soluble | Soluble |
GI | High | High | High | High | High | Low | High | Low | High | High | Low | Low | |
Log Kp (skin permeation) cm/s | −6.41 | −6.08 | −7.82 | −6.87 | −6.81 | −7.40 | −6.60 | −9.58 | −6.63 | −6.90 | −8.76 | −10.26 | |
Distribution | BBB permeant | Yes | No | No | Yes | No | No | No | No | No | No | No | No |
Metabolism | CYP1A2 inhibitor | No | No | No | No | No | Yes | Yes | No | No | Yes | No | No |
CYP2C19 inhibitor | No | No | No | No | No | No | No | No | No | No | No | No | |
CYP2C9 inhibitor | No | No | No | No | No | No | No | No | No | No | No | No | |
CYP2D6 inhibitor | No | Yes | No | Yes | No | No | Yes | No | No | Yes | No | No | |
CYP3A4 inhibitor | No | No | No | Yes | No | Yes | Yes | No | No | Yes | No | No | |
Druglikeness | Lipinski | Yes; 0 violation | Yes; 0 violation | Yes; 0 violation | Yes; 0 violation | Yes; 0 violation | Yes; 1 violation: NHorOH > 5 | Yes; 0 violation | No; 2 violations: NorO > 10, NHorOH > 5 | Yes; 0 violation | Yes; 0 violation | Yes; 1 violation: NHorOH > 5 | No; 3 violations: MW > 500, NorO > 10, NHorOH > 5 |
Metabolite Number | Classification | ||||
---|---|---|---|---|---|
Organ Toxicity (%Probability) | Toxicity Endpoint (% Probability) | ||||
Hepatotoxicity | Carcinogenicity | Immunotoxicity | Mutagenicity | Cytotoxicity | |
1 | Inactive (0.51) | Inactive (0.61) | Active (0.91) | Inactive (0.96) | Inactive (0.88) |
2 | Inactive (0.74) | Inactive (0.55) | Inactive (0.99) | Inactive (0.95) | Inactive (0.58) |
3 | Inactive (0.72) | Inactive (0.51) | Inactive (0.96) | Inactive (0.55) | Inactive (0.84) |
4 | Inactive (0.86) | Inactive (0.51) | Active (0.89) | Inactive (0.77) | Inactive (0.98) |
5 | Inactive (0.62) | Inactive (0.63) | Inactive (0.98) | Inactive (0.91) | Inactive (0.93) |
6 | Inactive (0.69) | Active (0.68) | Inactive (0.86) | Active (0.51) | Inactive (0.99) |
7 | Inactive (0.69) | Active (0.68) | Inactive (0.97) | Active (0.51) | Inactive (0.99) |
8 | Inactive (0.85) | Inactive (0.9) | Active (0.98) | Inactive (0.69) | Inactive (0.55) |
9 | Inactive (0.54) | Inactive (0.67) | Active (0.89) | Inactive (0.87) | Inactive (0.96) |
10 | Inactive (0.72) | Inactive (0.68) | Active (0.58) | Inactive (0.94) | Inactive (0.95) |
11 | Inactive (0.72) | Inactive (0.68) | Active (0.99) | Inactive (0.93) | Inactive (0.80) |
12 | Inactive (0.80) | Inactive (0.91) | Active (0.98) | Inactive (0.88) | Inactive (0.64) |
Metabolite Number | Prediction/Potency | Confidence | Probability Map |
---|---|---|---|
1 | Noncardiotoxic (−) | 80% | |
2 | Noncardiotoxic (−) | 60% | |
3 | Potentially cardiotoxic (+) | 50% | |
4 | Potentially cardiotoxic (+) | 50% | |
5 | Noncardiotoxic (−) | 80% | |
6 | Noncardiotoxic (−) | 60% | |
7 | Noncardiotoxic (−) | 50% | |
8 | Potentially cardiotoxic (+) | 50% | |
9 | Noncardiotoxic (−) | 80% | |
10 | Noncardiotoxic (−) | 60% | |
11 | Noncardiotoxic (−) | 50% | |
12 | Potentially cardiotoxic (+) | 60% |
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Mohammed, A.E.; Alghamdi, S.S.; Alharbi, N.K.; Alshehri, F.; Suliman, R.S.; Al-Dhabaan, F.; Alharbi, M. Limoniastrum monopetalum–Mediated Nanoparticles and Biomedicines: In Silico Study and Molecular Prediction of Biomolecules. Molecules 2022, 27, 8014. https://doi.org/10.3390/molecules27228014
Mohammed AE, Alghamdi SS, Alharbi NK, Alshehri F, Suliman RS, Al-Dhabaan F, Alharbi M. Limoniastrum monopetalum–Mediated Nanoparticles and Biomedicines: In Silico Study and Molecular Prediction of Biomolecules. Molecules. 2022; 27(22):8014. https://doi.org/10.3390/molecules27228014
Chicago/Turabian StyleMohammed, Afrah E., Sahar S. Alghamdi, Nada K. Alharbi, Fatma Alshehri, Rasha Saad Suliman, Fahad Al-Dhabaan, and Maha Alharbi. 2022. "Limoniastrum monopetalum–Mediated Nanoparticles and Biomedicines: In Silico Study and Molecular Prediction of Biomolecules" Molecules 27, no. 22: 8014. https://doi.org/10.3390/molecules27228014
APA StyleMohammed, A. E., Alghamdi, S. S., Alharbi, N. K., Alshehri, F., Suliman, R. S., Al-Dhabaan, F., & Alharbi, M. (2022). Limoniastrum monopetalum–Mediated Nanoparticles and Biomedicines: In Silico Study and Molecular Prediction of Biomolecules. Molecules, 27(22), 8014. https://doi.org/10.3390/molecules27228014