| Literature DB >> 29507318 |
Mengshan Li1, Huaijing Zhang2, Bingsheng Chen2, Yan Wu2, Lixin Guan2.
Abstract
The pKa value of drugs is an important parameter in drug design and pharmacology. In this paper, an improved particle swarm optimization (PSO) algorithm was proposed based on the population entropy diversity. In the improved algorithm, when the population entropy was higher than the set maximum threshold, the convergence strategy was adopted; when the population entropy was lower than the set minimum threshold the divergence strategy was adopted; when the population entropy was between the maximum and minimum threshold, the self-adaptive adjustment strategy was maintained. The improved PSO algorithm was applied in the training of radial basis function artificial neural network (RBF ANN) model and the selection of molecular descriptors. A quantitative structure-activity relationship model based on RBF ANN trained by the improved PSO algorithm was proposed to predict the pKa values of 74 kinds of neutral and basic drugs and then validated by another database containing 20 molecules. The validation results showed that the model had a good prediction performance. The absolute average relative error, root mean square error, and squared correlation coefficient were 0.3105, 0.0411, and 0.9685, respectively. The model can be used as a reference for exploring other quantitative structure-activity relationships.Entities:
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Year: 2018 PMID: 29507318 PMCID: PMC5838250 DOI: 10.1038/s41598-018-22332-7
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Figure 1Flowchart of CSAPSO-EDCD algorithm.
Experimental database.
| No. | Compounds | Experimental pKa |
|---|---|---|
| 1 | ergotamine | 6.3 |
| 2 | nefazodone | 6.5 |
| 3 | nizatidine | 6.59 |
| 4 | trazodone | 6.79 |
| 5 | mirtazapine | 7.3 |
| 6 | clozapine | 7.63 |
| 7 | domperidone | 7.9 |
| 8 | tolamolol | 7.9 |
| 9 | lidocaine | 7.94 |
| 10 | naloxone | 7.94 |
| 11 | quinidine | 8.05 |
| 12 | diltiazem | 8.06 |
| 13 | nicotine | 8.1 |
| 14 | perphenazine | 8.11 |
| 15 | butorphanol | 8.19 |
| 16 | codeine | 8.2 |
| 17 | nebivolol | 8.22 |
| 18 | galanthamine | 8.32 |
| 19 | fentanyl | 8.43 |
| 20 | ranitidine | 8.47 |
| 21 | oxycodone | 8.53 |
| 22 | cocaine | 8.7 |
| 23 | meperidine | 8.7 |
| 24 | timolol | 8.8 |
| 25 | remoxipride | 8.9 |
| 26 | verapamil | 8.92 |
| 27 | rivastigmine | 8.99 |
| 28 | promethazine | 9.1 |
| 29 | mexiletine | 9.15 |
| 30 | levomepromazine | 9.19 |
| 31 | betaxolol | 9.21 |
| 32 | trimipramine | 9.24 |
| 33 | chlorpromazine | 9.25 |
| 34 | chlorpheniramine | 9.26 |
| 35 | propafenone | 9.27 |
| 36 | flecainide | 9.3 |
| 37 | citalopram | 9.38 |
| 38 | clomipramine | 9.38 |
| 39 | labetalol | 9.4 |
| 40 | amitriptyline | 9.4 |
| 41 | propranolol | 9.45 |
| 42 | sumatriptan | 9.5 |
| 43 | venlafaxine | 9.5 |
| 44 | azelastine | 9.54 |
| 45 | pindolol | 9.54 |
| 46 | bisoprolol | 9.57 |
| 47 | alprenolol | 9.6 |
| 48 | acebutolol | 9.67 |
| 49 | nadolol | 9.67 |
| 50 | metoprolol | 9.7 |
| 51 | tacrine | 9.8 |
| 52 | tolterodine | 9.8 |
| 53 | atropine | 9.84 |
| 54 | terbutaline | 10 |
| 55 | atomoxetine | 10.1 |
| 56 | nortriptyline | 10.1 |
| 57 | desipramine | 10.23 |
| 58 | maprotiline | 10.5 |
| 59 | amantadine | 10.68 |
| 60 | cimetidine | 6.97 |
| 61 | sufentanil | 7.85 |
| 62 | clonidine | 8.05 |
| 63 | morphine | 8.18 |
| 64 | risperidone | 8.3 |
| 65 | haloperidol | 8.65 |
| 66 | azithromycin | 8.74 |
| 67 | diphenhydramine | 9.1 |
| 68 | procainamide | 9.24 |
| 69 | promazine | 9.28 |
| 70 | imipramine | 9.45 |
| 71 | paroxetine | 9.51 |
| 72 | atenolol | 9.6 |
| 73 | sotalol | 9.76 |
| 74 | quinacrine | 10.2 |
Parameters of the CSAPSO-EDCD algorithm.
| Parameters | Descriptions | Values |
|---|---|---|
| m | Number of particles | 50 |
| it | Iteration times | 2000 |
| min | Minimum error | 1.00E-07 |
| w | Inertia weight | Self-adaptive |
| c1 | Cognitive component | Generated by Lorenz chaotic operator |
| c2 | Social component | Generated by Lorenz chaotic operator |
Molecular descriptors selected by CSAPSO-EDCD algorithm.
| No. | Molecular descriptors | Descriptor types |
|---|---|---|
| 1 | Relative number of N atoms | Constitutional descriptors |
| 2 | Randic index (order 3) | Topological descriptors |
| 3 | RNCG relative negative charged (QMNEG/QTMINUS) [Quantum-Chemical PC] | Electrostatic descriptors |
| 4 | RNCS Relative negative charged SA (SAMNEG * RNCG) [Zefirov’s PC] | Electrostatic descriptors |
| 5 | Max net atomic charge | Quantum descriptors |
Figure 2Relationship between MSE and the number of hidden nodes.
Figure 3Correlations between predicted values and experimental data in the training set.
Figure 4Correlation between predicted values and experimental data in the testing set.
Statistical parameters of the proposed model.
| Sets |
|
|
|
|---|---|---|---|
| Training | 0.2316 | 0.0263 | 0.9873 |
| Testing | 0.3105 | 0.0411 | 0.9685 |
| Average | 0.2711 | 0.0337 | 0.9779 |
Additional testing database.
| NO. | Compounds | Experimental pKa |
|---|---|---|
| 1 | Guanidine | 13.8 |
| 2 | Clomipramine | 9.42 |
| 3 | Papaverine | 6.4 |
| 4 | Clotrimazole | 5.75 |
| 5 | Tryptophan | 9.1 |
| 6 | Methylamine | 10.62 |
| 7 | sec-Butylamine | 10.56 |
| 8 | Imipramine | 9.6 |
| 9 | n-Octylamine | 10.7 |
| 10 | Morpholine | 8.5 |
| 11 | Procaine | 9.11 |
| 12 | Guanethidine | 11.4 |
| 13 | Imidazo[2,3-b]thioxazole | 8 |
| 14 | Trimipramine | 9.39 |
| 15 | Dimethyl-iso-propylamine | 10.3 |
| 16 | tert-Butylcyclohexylamine | 11.23 |
| 17 | Sotalol | 9.3 |
| 18 | Alphaprodine | 8.7 |
| 19 | p-Toluidine | 5.1 |
| 20 | Nikethamide | 3.5 |
Figure 5Correlation between predicted values and experimental data in testing database.
Statistical results of the proposed model in testing database.
| AARD | RMSEP | R2 | |
|---|---|---|---|
| Max | 0.9857 | 0.1005 | 0.9992 |
| Min | 0.1243 | 0.06337 | 0.8786 |
| Average | 0.6656 | 0.0742 | 0.9212 |
Figure 6Correlation between prediction and experimental values of the comparison models.
Figure 7Residual curve for each comparison model.
Statistical results of each comparison model.
| Models | AARD | RMSEP | R2 | Average calculating time (S) | Average CPU utilization |
|---|---|---|---|---|---|
| RBF ANN | 1.0892 | 0.4002 | 0.8833 | 36 | 64% |
| PSO RBF ANN | 0.8898 | 0.1013 | 0.8952 | 57 | 75% |
| CSAPSO-EDCD RBF ANN | 0.3105 | 0.0411 | 0.9685 | 38 | 59% |