| Literature DB >> 31687555 |
Halima Hazhazi1, Nadjib Melkemi1, Toufik Salah1, Mohammed Bouachrine2,3.
Abstract
In the present work we have calculated several DFT reactivity descriptors for 1,2,4,5-Tetrazine at the B3LYP/6-311++G(d,p) level of theory in order to analyze its reactivity in vacuum and solvent phases. Whereas, the influence of the solvent was taken into account employing the PCM model. DFT-based descriptors such as (electronic chemical potential, electrophilicity, condensed Fukui function….) have been determined to predict the reactivity of 1,2,4,5-Tetrazine. A series of eighteen 1,2,4,5-Tetrazine derivatives was studied by using two computational techniques, namely, quantitative structure activity relationship (QSAR) and molecular docking. QSAR models of the antitumor activity of some 1,2,4,5-Tetrazine derivatives were established in gas and solvent phases which exhibited good statistical values for both cases. Whereas, multiple linear regression (MLR) procedure was used to obtain the best QSAR models and the leave-one-out (LOO) method to estimate the predictivity of our models. The most and the least active compounds were docked with the protein (3C4E) to confirm those obtained results from QSAR models and elucidate the binding mode between this type of compounds and corresponding protein.Entities:
Keywords: 1,2,4,5-Tetrazines; Antitumor activity; Bioinformatics; DFT; Molecular modeling; Pharmaceutical chemistry; QSAR; Solvent effect; Theoretical chemistry
Year: 2019 PMID: 31687555 PMCID: PMC6819827 DOI: 10.1016/j.heliyon.2019.e02451
Source DB: PubMed Journal: Heliyon ISSN: 2405-8440
Quantum chemical descriptors of 1,2,4,5-Tetrazine derivatives in both gas and aqueous phases.
| Comp. | Gas phase | Aqueous phase | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GAP | DM | qN1 | qC3 | qC6 | GAP | DM | qN1 | qC3 | qC6 | |||||||
| 1 | 0.594 | 0.712 | 1.508 | 0.151 | 2.280 | -0.387 | 0.413 | 0.409 | 0.417 | 0.321 | 1.284 | 0.155 | 3.691 | -0.384 | 0.428 | 0.412 |
| 2 | 0.389 | 0.308 | 0.174 | 0.128 | 3.862 | -0.308 | 0.363 | 0.402 | 0.385 | 0.329 | 0.214 | 0.131 | 5.429 | -0.297 | 0.369 | 0.424 |
| 3 | 0.547 | 0.624 | 0.185 | 0.151 | 1.912 | -0.389 | 0.413 | 0.410 | 0.269 | 0.292 | 1.466 | 0.155 | 3.285 | -0.386 | 0.428 | 0.412 |
| 4 | 0.612 | 0.694 | 0.230 | 0.142 | 2.557 | -0.389 | 0.408 | 0.406 | 0.381 | 0.404 | 0.192 | 0.146 | 3.868 | -0.387 | 0.424 | 0.407 |
| 5 | 0.490 | 0.559 | 0.233 | 0.148 | 2.296 | -0.388 | 0.412 | 0.408 | 0.284 | 0.306 | 0.217 | 0.151 | 3.695 | -0.385 | 0.427 | 0.410 |
| 6 | 0.195 | 0.114 | 0.095 | 0.105 | 0.000 | -0.476 | 0.406 | 0.406 | 0.194 | 0.122 | 0.107 | 0.106 | 0.000 | -0.477 | 0.413 | 0.413 |
| 7 | 0.176 | 0.175 | 0.002 | 0.128 | 0.000 | -0.201 | 0.347 | 0.346 | 0.174 | 0.173 | 0.002 | 0.130 | 0.000 | -0.208 | 0.359 | 0.359 |
| 8 | 0.328 | 0.170 | 0.072 | 0.168 | 1.595 | -0.490 | 0.419 | 0.419 | 0.259 | 0.130 | 0.394 | 0.176 | 2.519 | -0.50 | 0.425 | 0.425 |
| 9 | 0.194 | 0.114 | 0.090 | 0.104 | 0.000 | -0.477 | 0.404 | 0.423 | 0.194 | 0.120 | 0.098 | 0.103 | 0.000 | -0.476 | 0.429 | 0.410 |
| 10 | 0.200 | 0.122 | 0.074 | 0.09 | 0.000 | -0.480 | 0.409 | 0.409 | 0.196 | 0.132 | 0.091 | 0.096 | 0.000 | -0.482 | 0.417 | 0.417 |
| 11 | 0.379 | 0.391 | 1.373 | 0.150 | 3.826 | -0.382 | 0.416 | 0.396 | 0.214 | 0.209 | 1.307 | 0.155 | 5.901 | -0.372 | 0.432 | 0.404 |
| 12 | 0.412 | 0.382 | 1.413 | 0.150 | 3.621 | -0.382 | 0.414 | 0.396 | 0.243 | 0.209 | 1.382 | 0.155 | 5.667 | -0.374 | 0.429 | 0.404 |
| 13 | 0.456 | 0.396 | 0.355 | 0.151 | 3.637 | -0.379 | 0.414 | 0.399 | 0.256 | 0.213 | 0.316 | 0.156 | 5.768 | -0.370 | 0.429 | 0.406 |
| 14 | 0.413 | 0.432 | 0.142 | 0.142 | 3.732 | -0.390 | 0.320 | 0.388 | 0.258 | 0.257 | 0.132 | 0.147 | 5.859 | -0.374 | 0.397 | 0.400 |
| 15 | 0.475 | 0.466 | 0.150 | 0.142 | 3.366 | -0.390 | 0.318 | 0.388 | 0.305 | 0.279 | 0.146 | 0.146 | 5.438 | -0.381 | 0.334 | 0.395 |
| 16 | 0.489 | 0.429 | 0.147 | 0.142 | 3.620 | -0.390 | 0.317 | 0.391 | 0.307 | 0.260 | 0.132 | 0.147 | 5.729 | -0.380 | 0.333 | 0.397 |
| 17 | 0.455 | 0.461 | 0.163 | 0.143 | 4.826 | -0.389 | 0.318 | 0.381 | 0.290 | 0.296 | 0.149 | 0.147 | 7.314 | -0.375 | 0.339 | 0.388 |
| 18 | 0.347 | 0.200 | 0.106 | 0.105 | 2.220 | -0.359 | 0.421 | 0.414 | 0.645 | 0.477 | 0.050 | 0.102 | 5.132 | -0.362 | 0.376 | 0.417 |
Reactivity descriptors for 1,2,4,5-Tetrazine at theB3LYP/6–311++G(d,p) level.
| Et (eV) | HOMO (eV) | LUMO (eV) | ΔE (eV) | η (eV) | μ (eV) | DM (Debye) | ||
|---|---|---|---|---|---|---|---|---|
| Gas phase | -8095.563 | -5.848 | -0.843 | 5.005 | 5.004 | -3.345 | 1.115 | 0.846 |
| Aqueous phase | -8095.889 | -5.984 | -0.897 | 5.087 | 5.086 | -3.427 | 1.154 | 1.085 |
Fukui function values of 1,2,4,5-Tetrazine in gas and aqueous phases.
| Atoms | Gas phase | Aqueous phase | ||
|---|---|---|---|---|
| f (-) | f(+) | f (-) | f(+) | |
| N1 | 0.1967 | 0.0261 | 0.2103 | 0.0366 |
| N2 | 0.1481 | 0.0350 | 0.1524 | 0.1627 |
| C3 | 0.0405 | 0.0363 | 0.0449 | 0.2429 |
| N4 | 0.1967 | 0.0261 | 0.2103 | 0.0366 |
| N5 | 0.1481 | 0.0350 | 0.1524 | 0.1627 |
| C6 | 0.0405 | 0.0363 | 0.0449 | 0.2429 |
| H7 | 0.0578 | 0.2158 | 0.0445 | 0.0352 |
| H8 | 0.0569 | 0.1871 | 0.0480 | 0.0222 |
| H9 | 0.0578 | 0.2151 | 0.0442 | 0.0352 |
| H10 | 0.0570 | 0.1864 | 0.0480 | 0.0222 |
Fig. 1Electron-density mapped f (+) and f (-) Fukui function for 1,2,4,5-Tetrazine in both gas and aqueous phases (the blue regions show the areas of the molecules most susceptible to nucleophilic attacks and the red regions show the areas of the molecules most susceptible to electrophilic attacks).
Fig. 2Chemical structures and experimental activity of the 1,2,4,5-Tetrazine derivatives under study.
Cross-validation parameters in both gas and aqueous phases.
| Model | PRESS | SSY | SPRESS | |||
|---|---|---|---|---|---|---|
| (1) | 0.215 | 1.241 | 0.173 | 0.119 | 0.697 | 0.827 |
| (2) | 0.618 | 3.753 | 0.164 | 0.202 | 0.712 | 0.835 |
Experimental, predicted and residual activity of 1,2,4,5-Tetrazine derivatives in gas and aqueous phases.
| Comp. | pIC50Exp | Gas phase | Aqueous phase | ||
|---|---|---|---|---|---|
| pIC50Pred | Residue | pIC50Pred | Residue | ||
| 1 | 4.403 | 4.298 | 0.104 | 4.111 | 0.292 |
| 2 | 4.389 | 4.303 | 0.085 | 4.578 | -0.189 |
| 3 | 4.306 | 4.441 | -0.135 | 4.745 | -0.390 |
| 4 | 4.701 | 4.694 | 0.006 | 6.074 | 0.165 |
| 6 | 4.398 | 4.408 | -0.010 | 4.549 | 0.151 |
| 7 | 4.286 | 4.198 | 0.087 | 4.355 | 0.042 |
| 8 | 4.286 | 4.429 | -0.143 | 4.411 | -0.125 |
| 9 | 4.879 | 4.789 | 0.089 | 4.622 | -0.362 |
| 10 | 4.350 | 4.399 | -0.049 | 4.652 | 0.226 |
| 11 | 4.316 | 4.368 | -0.052 | 4.390 | -0.040 |
| 12 | 5.011 | 4.863 | 0.147 | 4.103 | 0.212 |
| 15 | 5.020 | 4.866 | 0.153 | 4.804 | 0.215 |
| 16 | 4.500 | 4.800 | -0.300 | 4.592 | -0.092 |
| 17 | 5.069 | 5.082 | -0.013 | 5.109 | -0.040 |
| 18 | 4.348 | 4.316 | 0.031 | 4.440 | -0.092 |
Fig. 3a) Predicted plots versus experimental observed antitumor activity for model in gas. b) Predicted plots versus experimental observed antitumor activity for model in aqueous phase.
Fig. 4a) Plots of residual against experimental observed in gas. b) Plots of residual against experimental observed in aqueous phase.
Fig. 5Interactions between the protein 3C4E and the most active compound (4).
Fig. 6Interactions between the protein 3C4E and the least active compound (8).
Fig. 7Interactions between the protein 3C4E and the least active compound (9).