Identification of a Family of Glycoside Derivatives Biologically Active against Acinetobacter baumannii and Other MDR Bacteria Using a QSPR Model
Abstract
:1. Introduction
2. Results and Discussion
2.1. QSPR Model Validation
2.2. QSPR Interpretation
2.3. Virtual Screening Using BIOFACQUIM Dataset
2.4. Antibacterial Activity Evaluation
2.5. Glycoside SAR Analysis
3. Materials and Methods
3.1. Data Set
3.2. Calculation of Molecular Descriptors
3.3. Generation of the Mathematical Model
3.4. QSPR Validation of Prediction Capability
3.5. External Validation
3.6. Virtual Screening
3.7. Plant Material
3.8. Extraction and Isolation of Compounds
3.9. Bacterial Strains
3.10. Antibacterial Assays
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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MolID | MW | D/Dr06 | GATS6m | nROR | nHDon | nHBonds | C018 | H051 | N075 | TI2 | pMIC |
---|---|---|---|---|---|---|---|---|---|---|---|
26 | 274.24 | 101.297 | 0.399 | 1 | 1 | 0 | 1 | 0 | 0 | 1.208 | 5.910 |
27 | 404.51 | 208.41 | 1.05 | 5 | 2 | 2 | 0 | 0 | 0 | 3.678 | 5.533 |
28 | 1167.41 | 1692.143 | 0.951 | 12 | 16 | 8 | 0 | 2 | 0 | 8.304 | 9.049 |
29 | 1195.47 | 1739.777 | 0.958 | 12 | 16 | 8 | 0 | 2 | 0 | 8.397 | 9.076 |
30 | 1341.63 | 2360.184 | 0.965 | 13 | 19 | 10 | 0 | 2 | 0 | 10.723 | 9.756 |
31 | 1690.16 | 2257.102 | 1.01 | 14 | 13 | 8 | 0 | 9 | 0 | 6.18 | 8.879 |
32 | 2473.43 | 6328.172 | 1.071 | 19 | 16 | 11 | 0 | 10 | 0 | 20.998 | 12.845 |
33 | 2449.3 | 7015.971 | 1.082 | 19 | 16 | 11 | 0 | 8 | 0 | 21.234 | 13.451 |
34 | 2445.37 | 6531.924 | 1.071 | 19 | 16 | 11 | 0 | 10 | 0 | 21.416 | 12.972 |
35 | 2501.49 | 6713.547 | 1.076 | 19 | 16 | 9 | 0 | 10 | 0 | 21.566 | 13.485 |
36 | 272.27 | 101.297 | 0.894 | 1 | 0 | 0 | 1 | 0 | 0 | 1.208 | 5.579 |
37 | 346.31 | 89.966 | 1.133 | 2 | 1 | 0 | 1 | 0 | 0 | 1.397 | 5.920 |
38 | 560.71 | 440.654 | 0.966 | 4 | 8 | 4 | 0 | 0 | 0 | 5.474 | 5.695 |
39 | 250.27 | 80.687 | 0.942 | 1 | 2 | 1 | 1 | 0 | 0 | 1.546 | 5.580 |
40 | 1151.41 | 1669.117 | 0.921 | 11 | 16 | 9 | 0 | 2 | 0 | 8.266 | 8.511 |
41 | 1179.47 | 1715.713 | 0.923 | 11 | 16 | 9 | 0 | 2 | 0 | 8.347 | 8.539 |
42 | 869.18 | 889.623 | 0.957 | 7 | 10 | 5 | 0 | 2 | 0 | 8.006 | 6.834 |
43 | 1035.28 | 1396.119 | 0.967 | 10 | 14 | 8 | 0 | 2 | 0 | 8.601 | 7.984 |
44 | 1165.44 | 1695.422 | 0.921 | 11 | 15 | 10 | 0 | 2 | 0 | 8.575 | 8.216 |
45 | 1193.5 | 1742.017 | 0.923 | 11 | 15 | 9 | 0 | 2 | 0 | 8.623 | 8.446 |
46 | 250.27 | 80.687 | 0.942 | 1 | 2 | 1 | 1 | 0 | 0 | 1.546 | 5.580 |
47 | 1199.65 | 1656.598 | 1.024 | 10 | 10 | 7 | 0 | 4 | 0 | 8.71 | 7.644 |
48 | 1223.67 | 1189.333 | 1.054 | 10 | 8 | 6 | 0 | 5 | 0 | 5.649 | 7.156 |
49 | 512.56 | 409.063 | 0.805 | 3 | 6 | 2 | 1 | 2 | 1 | 4.621 | 6.430 |
50 | 302.36 | 106.192 | 1.753 | 5 | 2 | 1 | 0 | 0 | 0 | 1.027 | 5.304 |
51 | 1369.82 | 1718.197 | 1.079 | 10 | 8 | 6 | 0 | 5 | 0 | 6.149 | 7.460 |
52 | 1383.85 | 1778.609 | 1.097 | 10 | 8 | 6 | 0 | 6 | 0 | 6.324 | 7.386 |
53 | 2795.76 | 9251.423 | 1.099 | 20 | 16 | 8 | 0 | 10 | 0 | 22.254 | 15.481 |
MolID | MW | D/Dr06 | GATS6m | nROR | nHDon | nHBonds | H051 | TI2 | pMIC |
---|---|---|---|---|---|---|---|---|---|
54 | 1139.49 | 637.544 | 1.05 | 8 | 8 | 4 | 5 | 4.452 | 6.553 |
55 | 1095.43 | 603.051 | 1.06 | 8 | 7 | 4 | 5 | 4.134 | 6.406 |
56 | 1155.49 | 645.374 | 1.047 | 8 | 9 | 4 | 5 | 4.4 | 6.672 |
57 | 1225.64 | 1192.314 | 1.016 | 10 | 9 | 5 | 7 | 5.92 | 7.289 |
58 | 1107.49 | 600.453 | 1.072 | 8 | 6 | 5 | 5 | 4.095 | 6.080 |
59 | 1153.38 | 1669.117 | 0.957 | 12 | 16 | 11 | 2 | 8.266 | 8.422 |
60 | 334.46 | 90.65 | 0.904 | 2 | 4 | 3 | 2 | 4.886 | 4.374 |
61 | 326.33 | 164.888 | 1.054 | 1 | 5 | 1 | 0 | 4.222 | 4.733 |
62 | 342.33 | 166.979 | 1.09 | 1 | 6 | 2 | 0 | 3.98 | 4.624 |
63 | 1646.15 | 2393.949 | 1.019 | 13 | 14 | 12 | 6 | 5.644 | 8.223 |
64 | 1019.28 | 1307.203 | 0.962 | 10 | 13 | 6 | 2 | 9.197 | 8.242 |
65 | 855.1 | 437.562 | 0.955 | 8 | 9 | 5 | 2 | 3.704 | 6.688 |
66 | 1093.46 | 601.959 | 1.069 | 8 | 6 | 4 | 5 | 4.081 | 6.285 |
67 | 1037.39 | 565.718 | 1.019 | 8 | 7 | 4 | 5 | 4.448 | 6.410 |
68 | 1123.49 | 624.213 | 1.054 | 8 | 7 | 4 | 5 | 4.266 | 6.424 |
Bacterial Strains | |||||||||
---|---|---|---|---|---|---|---|---|---|
IDSample | E. coli ATCC 25922 | S aureus ATCC | A baumannii 9736 (1) | A. baumannii 10324 | E. coli 10225 | K. pneumoniae 6411 | K. pneumoniae3407−2 | P. aeruginosa 4899 | P. aeruginosa 4677 |
54 | − | − | − | − | − | + | − | − | − |
55 | − | + | − | − | − | + | − | + | + |
56 | + | + | + | − | − | + | + | + | + |
58 | − | − | − | − | − | − | + | − | − |
60 | + | + | + | + | + | + | + | + | + |
61 | − | − | − | + | − | − | − | − | − |
62 | − | − | − | + | − | − | − | − | − |
63 | − | − | + | + | − | − | − | − | − |
64 | − | − | + | − | − | − | − | − | − |
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Palacios-Can, F.J.; Silva-Sánchez, J.; León-Rivera, I.; Tlahuext, H.; Pastor, N.; Razo-Hernández, R.S. Identification of a Family of Glycoside Derivatives Biologically Active against Acinetobacter baumannii and Other MDR Bacteria Using a QSPR Model. Pharmaceuticals 2023, 16, 250. https://doi.org/10.3390/ph16020250
Palacios-Can FJ, Silva-Sánchez J, León-Rivera I, Tlahuext H, Pastor N, Razo-Hernández RS. Identification of a Family of Glycoside Derivatives Biologically Active against Acinetobacter baumannii and Other MDR Bacteria Using a QSPR Model. Pharmaceuticals. 2023; 16(2):250. https://doi.org/10.3390/ph16020250
Chicago/Turabian StylePalacios-Can, Francisco José, Jesús Silva-Sánchez, Ismael León-Rivera, Hugo Tlahuext, Nina Pastor, and Rodrigo Said Razo-Hernández. 2023. "Identification of a Family of Glycoside Derivatives Biologically Active against Acinetobacter baumannii and Other MDR Bacteria Using a QSPR Model" Pharmaceuticals 16, no. 2: 250. https://doi.org/10.3390/ph16020250
APA StylePalacios-Can, F. J., Silva-Sánchez, J., León-Rivera, I., Tlahuext, H., Pastor, N., & Razo-Hernández, R. S. (2023). Identification of a Family of Glycoside Derivatives Biologically Active against Acinetobacter baumannii and Other MDR Bacteria Using a QSPR Model. Pharmaceuticals, 16(2), 250. https://doi.org/10.3390/ph16020250