Submitted:
29 March 2024
Posted:
29 March 2024
You are already at the latest version
Abstract
Keywords:
1. Introduction
2. Materials and Methods
2.1. Materials
2.1.1. Phytochemistry
2.1.2. Flavonoids
2.1.3. Phenolic Glycosides
2.1.4. Non-Phenolic Glycosides

2.1.5. Organic Acids

2.1.6. Simple Phenolics

2.1.7. Sterols and Terpenes

2.1.8. Lignans

2.1.9. Volatiles

2.1.10. Pharmacological Activity
2.1.11. Anti-Inflammatory Activity
2.1.12. HPLC Method
2.2. Methods


3.2.1. Extraction Method for a Aqueous Extracts
3.2.2. Antimicrobial Assay
2.3. Procedure for Molecular Docking
3. Results
3.1. Experimental Antimicrobial Activity Results

3.2. Molecular Docking Studies Results
3.2.1. Results on Escherichia coli Simulations
3.2.2. Results on Staphylococcus aureus Simulations
3.2.3. Results on Candida albicans Simulations
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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| Ligand | Score | RMSD (Å) |
Amino acids group interaction |
Hydrogen bond |
Bond Length (Å) |
|---|---|---|---|---|---|
| NOV | -51.89 | 0.77 | ASP 1077, ARG 1132, PRO 1075, ALA 1086, MET 1074, ARG 1072, GLY 1073, THR 1163, ILE 1090, ASP 1069, GLY 1071, GLU 1046, ASN 1042, SER 1043, ASP 1045 | O sp3 (O3) – O sp2 ASP 1077 O sp3 (O3) – O sp2 ASP 1077 O sp3 (O11) – N sp2 ARG 1132 O sp3 (O11) – N sp2 ARG 1132 N sp3(N1) – O sp2 ASP 1069 O sp3 (O6) – O sp2 ASN 1042 |
3.122 2.686 3.152 3.106 2.645 2.730 |
| Salicin | -49.75 | 0.06 | LEU 1091, ILE 1090, VAL 1039, VAL 1067, ASN 1042, VAL 1165, SER 1043, SER 1164, ASP 1069, GLU 1046, THR 1163, MET 1074, GLY 1162, GLY 1071, GLY 1073, ARG 1072, PRO 1075, ARG 1132. | O sp3 (O7) – O sp3 SER 1043 O sp3 (O7) – N sp2 SER 1043 O sp3 (O7) – O sp2 ASP 1069 O sp3 (O5) – O sp2 ASP 1069 O sp3 (O5) – O sp2 ASP 1069 O sp3 (O5) – O sp3 THR 1163 O sp3 (O3) – O sp2 GLU 1046 O sp3 (O3) – N sp2 ARG 1072 O sp3 (O3) – N sp2 GLY 1073 O sp3 (O4) – O sp2 GLY 1073 |
2.678 3.200 3.100 2.824 3.286 2.656 2.660 2.950 2.780 3.044 |
| Ligand | Score | Group interaction |
Hydrogen bond |
Bond Length, (Å) |
Steric interactions | Distance (Å) |
|---|---|---|---|---|---|---|
| NOV | -100.89 |
ALA 1086, ARG 1072, ARG 1132, ASN 1042, ASP 1045, ASP 1069, ASP 1077, GLU 1046, GLY 1073, ILE 1090, MET 1074, PRO 1075, SER 1043, THR1163 | O sp3 (O1) – O sp2 ASN 1042 N sp2(N1) – O sp2 ASP 1069 O sp3 (O3) – O sp3 ASP 1077 O sp3 (O11) – N sp2 ARG 1132 O sp2 (O11) – N sp2 ARG 1132 |
2.729 2.645 2.685 3.105 3.152 |
C sp2 (C18) – N sp2 ARG 1077 C sp2 (C8) – N sp2 ARG 1072 |
3.17 3.16 |
| Salicin |
-98.29 |
ARG 1072, ARG 1132, ASN 1042, ASP 1069, GLU 1046, GLY 1071, GLY 1073, GLY 1162, ILE 1090, MET 1074, PRO 1075, SER 1043, THR 1163, VAL 1039, VAL 1067, VAL 1165 | O sp3 (O7) – O sp2 VAL 1039 O sp3 (O7) – O sp3 SER 1043 O sp3 (O5) – O sp2 ASP 1069 O sp3 (O5) – O sp3 THR 1063 O sp3 (O3) – N sp2 GLY 1073 O sp3 (O3) - N sp2 ARG 1072 O sp3 (O3) - O sp2 GLU 1046 O sp3 (O3) - O sp2 GLY 1073 |
2.735 2.818 2.835 2.601 2.743 2.942 2.617 3.082 |
C sp3 (C12) – C sp3 MET 1074 O sp3 (O5) – C sp3 THR 1163 O sp3 (O3) – C sp3 GLU 1046 O sp3 (O3) – C sp2 GLU 1046 |
3.150 2.933 3.063 2.903 |
| Ligand | Score | RMSD | Group interaction |
Hydrogen bond |
Bond Length (Å) |
|---|---|---|---|---|---|
| CPF | -80.60 | 0.67 | ASP 437, SER 1085, SER 1084, GLY 1082, GLY 459, LYS 460, ARG 458, GLU 477, DA 13:H, DC 12:H | O sp2 (O1) – O sp3 SER 1084:B O sp2 (O2) – O sp3 SER 1084:B |
2.489 2.604 |
| Salcin | -64.52 | 0.44 | ASP 437, SER 1084, GLY 459, DT 10:G, DG 9:G, DT 8:E, DG 7:E, DA 13:H, DC 12>H | O sp3 (O7) – O sp2 DT 8:E O sp3 (O7) – N sp2 DA 13:H O sp3 (O5) – O sp3 DG 9:G O sp3 (O4) – O sp3 DG 9:G O sp3 (O4) – O sp2 DC 12:H O sp3 (O3) – O sp3 DA 13:H |
2.881 3.016 2.844 3.069 3.006 3.070 |
| Ligand | Mol Dock Score | Molecule Contributions | Hydrogen bond |
Bond Length (Å) |
Electrostatic interactions / Steric interactions | Distance (Å) |
|---|---|---|---|---|---|---|
| CPF | -121.47 | ARG 458:B, ASP 512:B, ASP 1083:B, GLU 1088:B, GLY 459:B, GLY 1082:B, LYS 417:B, LYS 460:B, LYS 1043:B, SER 1084:B, ARG 1122:D, LYS 1066:D, *DA…DA:G, **DT. DA:H. | O sp2 (O1) – O sp3 SER 1084:B |
2.489 | Electrostatic interactions O sp2 (O1) – Mn O sp2 (O2) – Mn |
2.089 4.409 |
| Steric interactions O sp2 (O2) – C sp3 from SER 1084:B C sp2 (C3) – O sp3 from SER 1084:B C sp3 (C16) – C sp3 from ARG 458:B |
3.024 2.932 3.152 |
|||||
| Salicin | -94.21 | ARG 458:B, ASN 476:B, ASP 437:B, GLU 477:B, GLY 459:B, *DA…DA:G, **DT. DA:H. | O sp3 (O7) – O sp3 ASP 437:B O sp3 (O7) – O sp2 ASP 437:B O sp3 (O7) – O sp3 *DA…DA:G O sp3 (O5) – N sp2 *DA…DA:G O sp3 (O5) – O sp3 **DT. DA:H O sp3 (O3) – O sp2 ARG 458:B O sp3 (O6) – O sp2 GLU 477:B O sp3 (O6) – O sp3 **DT. DA:H O sp3 (O6) – N sp2 **DT. DA:H |
3.190 2.996 3.226 2.460 2.950 3.094 3.168 3.052 3.429 |
C sp3 (C9) – N sp2 ARG 458:B C sp3 (C13) – O sp2 GLU 477:B |
2.695 3.219 |
| Ligand | Score | RMSD (Å) |
Group interaction | Hydrogen Bond | Bond Length (Å) |
|---|---|---|---|---|---|
| Co-crystallized NDP |
-79.35 | 2.86 | LEU 121, GLU 120, SER 95, TYR 118, GLU 116, ILE 117, SER 94, ARG 79, ILE 9, ALA 93, VAL 10, SER 78, LEU 77, ILE 112, GLY 113, MET 54, ALA 11, GLY 114, ILE 19, THR 147, GLY 20, TYR 21, PHE 36, ARG 56, LYS 57, THR 58, MET 25, GLY 23, PRO 26, LYS 24 | N sp2 (N7N) – O sp2 ILE 112 O sp3 (O2D) – O sp2 ILE 19 O sp3 (O4D) – N sp2 ALA 115 O sp3 (O5D) – N sp2 ALA 115 O sp2 (O2N) – O sp3 THR 58 O sp2 (O2N – N sp2 THR 58 O sp2 (O2A) – N sp2 ALA 115 O sp2 (O2A) – N sp2 GLU 116 O sp3 (O3B) – O sp2 GLU 116 O sp3 (O3B) – N sp3 LYS 57 O sp2 (O2X) – N sp3 LYS 57 O sp2 (O2X) – N sp2 ARG 56 O sp2 (O1X) – N sp2 ARG 79 O sp2 (O3X) – N sp2 ARG 79 O sp2 (O3X) – N sp2 ARG 79 N sp2 (N3A) – N sp2 SER 78 |
3.069 2.649 3.335 3.394 2.977 3.194 3.111 2.733 2.892 2.924 2.772 2.365 2.698 2,984 3.061 3.286 |
| Salicin | -57.52 | 0.26 | SER 89, ARG 79, GLU 120, LEU 121, ILE 96, GLU 116, SER 95, SER 94, SER 78, SER 80, LEU 77, GLY 55, ALA 93, ARG 56, LYS 57, THR 58, MET 54 | O sp3 (O7) - O sp3 GLU 116 O sp3 (O7) – N sp2 ARG 79 O sp3 (O7) – N sp2 ARG 79 O sp3 (O5) – N sp2 ARG 79 O sp3 (O5) – N sp2 ARG 79 O sp3 (O3) – N sp2 ARG 56 O sp3 (O4) – N sp2 ARG 56 O sp3 (O4) – N sp3 LYS 57 O sp3 (O4) – N sp2 LYS 57 O sp3 (O6) – N sp2 LYS 57 O sp3 (O6) – N sp2 ARG 56 O sp3 (O2) – N sp2 ARG 79 O sp3 (O2) – N sp2 ARG 79 O sp3 (O2) – N sp2 ARG 79 |
3.096 3.157 3.045 2.642 2.727 2.608 3.246 3.295 3.123 2.875 3.116 3.174 3.066 3.145 |
| Ligand | Mol Dock Score | Molecule contributions | Hydrogen bond |
Bond Length (Å) |
Electrostatic interactions / Steric interactions | Distance (Å) |
|---|---|---|---|---|---|---|
| Co-crystallized NDP | -155.24 | ALA 11, ALA 12, ALA 93, ALA 115, ARG 49, ARG 56, ARG 67, ARG 72, ARG 79, ARG 191, ASP 87, ASP 146, GLU 32, GLU 60, GLU 82, GLU 84, GLU 97, GLU 116, GLU 120, GLY 20, GLY 23, GLY 55, GLY 113, GLY 114, HIS 92, ILE 19, ILE 112, ILE 117, LEU 77, LEU 121, LYS 3, LYS 14, LYS 22, LYS 24, LYS 31, LYS 37, LYS 45, LYS 57, LYS 65, LYS 150, LYS 158, LYS 178, LYS 192, MET 25, SER 78, SER 80, SER 94, SER 95, THR 58, THR 147, TRP 27, TYR 21, TYR 118, VAL 10 | N sp2 (N7N) – O sp2 ILE 19 N sp2 (N7N) – O sp2 ALA 11 O sp3 (O7N) – N sp2 ALA 11 O sp3 (O7N) – N sp2 ALA 11 O sp3 (O4D) – N sp2 ALA 115 O sp3 (O5D) – N sp2 ALA 115 O sp2 (O2A) – N sp2 GLY 114 O sp2 (O2A) – O sp3 THR 58 O sp2 (O2A) – N sp2 THR 58 O sp2 (O2N) – N sp2 GLU 116 O sp2 (O1A) – N sp2 GLU 116 O sp2 (O1A) – N sp2 ILE 117 O sp3 (O3B) – N sp3 LYS 57 O sp2 (O2X) – N sp2 ARG 56 O sp2 (O1X) – N sp2 ARG 56 O sp2 (O1X) – O sp3 SER 78 O sp2 (O3X) – N sp2 ARG 79 O sp2 (O3X) – N sp2 ARG 79 |
3.204 2.887 3.093 3.514 3.437 2.930 2.813 2.565 3.218 3.109 3.405 3.302 2.585 3.199 2.893 2.455 2.757 2.545 |
Electrostatic interactions O sp2 (O2X) – N sp2 ARG 79 O sp2 (O2X) – N sp2 ARG 56 O sp3 (O2X) – N sp3 LYS 57 O sp2 (O1X) – N sp2 ARG 79 O sp2 (O1X) – N sp2 ARG 79 O sp2 (O3X) – N sp2 ARG 56 |
3.716 3.199 4.399 2.545 4.247 3.681 |
| Steric interactions O sp2 (O1A) – N sp2 GLY 114 O sp2 (O2A) – C sp3 GLY 114 O sp2 (O1X) – C sp3 SER 78 |
3.109 3.181 3.153 |
|||||
| Salicin | - 94.82 | ARG 56, ARG 79, GLU 116, GLU 120, GLY 55, ILE 117, LEU 77, LEU 121, LYS 57, SER 78, SER 94, SER 95 | O sp3 (O7) - O sp3 GLU 116 O sp3 (O7) – N sp2 ARG 79 O sp3 (O7) – N sp2 ARG 79 O sp3 (O5) – N sp2 ARG 79 O sp3 (O5) – N sp2 ARG 79 O sp3 (O3) – N sp2 ARG 56 O sp3 (O4) – N sp2 ARG 56 O sp3 (O4) – N sp2 LYS 57 O sp3 (O4) – O sp2 GLU 116 |
2.810 3.000 3.052 2.961 2.909 3.318 2.855 2.798 3.110 |
O sp3 (O4) – C sp3 LYS 57 | 2.939 |
| Compounds | Atoms | Weight [Daltons] |
Flexible bonds |
Lipinski violations | Hydrogen donors |
Hydrogen acceptors | Log P |
|---|---|---|---|---|---|---|---|
| Salicin | 38 | 286.28 | 4 | 0 | 5 | 7 | 1.68 |
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