Chemoinformatics Studies on a Series of Imidazoles as Cruzain Inhibitors
Abstract
:1. Introduction
2. Materials and Methods
2.1. QSAR and Molecular Modeling Tools
2.2. Dataset
2.3. Molecular Docking
2.4. QSAR Modeling
2.5. Applicabilty Domain
3. Results and Discussion
3.1. HQSAR and AutoQSAR Models
3.2. CoMFA and CoMSIA Models
3.3. Applicability Domain
3.4. 2D Contribution Maps
3.5. 3D Contour Maps
4. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Inhibitor | Structure | pIC50 a |
---|---|---|
1 | | 6.00 |
2 * | | 6.92 |
3 | | 6.44 |
4 * | | 6.39 |
5 | | 6.30 |
6 | | 6.30 |
7 | | 6.28 |
8 | | 6.24 |
9 * | | 6.22 |
10 | | 6.22 |
11 | | 6.18 |
12 * | | 6.15 |
13 | | 6.12 |
14 | | 6.68 |
15 | | 5.77 |
16 * | | 5.74 |
17 | | 5.74 |
18 | | 5.70 |
19 | | 5.60 |
20 | | 5.55 |
21 * | | 5.52 |
22 | | 5.51 |
23 | | 5.49 |
24 | | 5.49 |
25 * | | 5.32 |
26 | | 5.21 |
27 * | | 5.21 |
28 | | 4.11 |
29 | | 4.00 |
30 * | | 4.00 |
31 | | 4.00 |
32 | | 4.00 |
33 | | 4.00 |
34 | | 4.00 |
35 | | 4.00 |
36 * | | 4.00 |
37 | | 4.00 |
Model | Fragment Distinction | q2 | r2 | SEE | HL | N |
---|---|---|---|---|---|---|
1 | A/B/C | 0.70 | 0.92 | 0.28 | 199 | 3 |
2 | A/B/C/Ch | 0.70 | 0.92 | 0.28 | 199 | 3 |
3 | A/B/C/H | 0.72 | 0.90 | 0.33 | 83 | 4 |
4 | A/B/C/H/Ch | 0.72 | 0.90 | 0.33 | 83 | 4 |
Model | Fragment Distinction | Fragment Size | q2 | r2 | r2pred | SEE | HL | N |
---|---|---|---|---|---|---|---|---|
5 | A/B/C | 2–7 | 0.70 | 0.92 | 0.78 | 0.27 | 199 | 3 |
6 | A/B/C | 3–7 | 0.71 | 0.92 | 0.80 | 0.28 | 199 | 3 |
8 | A/B/C/H | 2–6 | 0.76 | 0.90 | 0.67 | 0.33 | 83 | 4 |
7 | A/B/C/Ch | 3–7 | 0.70 | 0.92 | 0.78 | 0.28 | 199 | 3 |
9 | A/B/C/H/Ch | 2–6 | 0.76 | 0.90 | 0.67 | 0.33 | 83 | 4 |
Inhibitor | Experimental | HQSAR | AutoQSAR | CoMFA | CoMSIA | ||||
---|---|---|---|---|---|---|---|---|---|
Predicted | Residual 1 | Predicted | Residual 1 | Predicted | Residual 1 | Predicted | Residual 1 | ||
1 | 6.00 | 5.34 | 0.66 | 5.49 | 0.51 | 5.78 | 0.22 | 5.85 | 0.15 |
2 * | 6.92 | 6.25 | 0.67 | 6.38 | 0.54 | 6.08 | 0.84 | 6.27 | 0.65 |
3 | 6.44 | 6.02 | 0.42 | 6.27 | 0.17 | 6.47 | −0.03 | 6.46 | −0.02 |
4 * | 6.39 | 5.96 | 0.43 | 5.98 | 0.41 | 6.01 | 0.38 | 6.05 | 0.34 |
5 | 6.30 | 6.14 | 0.16 | 6.24 | 0.06 | 6.32 | −0.02 | 6.01 | 0.29 |
6 | 6.30 | 6.49 | −0.19 | 6.30 | 0.00 | 6.42 | −0.12 | 6.08 | 0.22 |
7 | 6.28 | 5.93 | 0.35 | 5.85 | 0.43 | 6.28 | 0.00 | 6.21 | 0.07 |
8 | 6.24 | 5.90 | 0.34 | 6.23 | 0.01 | 6.25 | −0.01 | 6.02 | 0.22 |
9 * | 6.22 | 6.60 | −0.38 | 6.11 | 0.11 | 6.04 | 0.18 | 5.93 | 0.29 |
10 | 6.22 | 5.99 | 0.23 | 6.04 | 0.18 | 6.19 | 0.03 | 6.16 | 0.06 |
11 | 6.18 | 6.07 | 0.11 | 6.36 | −0.18 | 6.17 | 0.01 | 6.09 | 0.09 |
12 * | 6.15 | 5.65 | 0.50 | 5.99 | 0.16 | 6.04 | 0.11 | 6.16 | −0.01 |
13 | 6.12 | 5.93 | 0.19 | 5.95 | 0.17 | 6.12 | 0.00 | 6.13 | −0.01 |
14 | 6.68 | 6.90 | −0.22 | 6.06 | 0.62 | 6.67 | 0.01 | 6.53 | 0.15 |
15 | 5.77 | 5.83 | −0.06 | 6.19 | −0.42 | 5.68 | 0.09 | 5.75 | 0.02 |
16 * | 5.74 | 5.81 | −0.07 | 6.10 | −0.36 | 6.10 | −0.36 | 6.04 | −0.30 |
17 | 5.74 | 5.93 | −0.19 | 6.04 | −0.30 | 5.79 | −0.05 | 5.79 | −0.05 |
18 | 5.70 | 5.91 | −0.21 | 5.53 | 0.17 | 5.71 | −0.01 | 5.79 | −0.09 |
19 | 5.60 | 5.80 | −0.20 | 5.99 | −0.39 | 5.67 | −0.07 | 5.80 | −0.20 |
20 | 5.55 | 5.92 | −0.37 | 5.76 | −0.21 | 5.61 | −0.06 | 6.03 | −0.48 |
21 * | 5.52 | 5.82 | −0.30 | 5.85 | −0.33 | 5.55 | −0.03 | 5.87 | −0.35 |
22 | 5.51 | 5.93 | −0.42 | 5.78 | −0.27 | 5.56 | −0.05 | 5.85 | −0.34 |
23 | 5.49 | 5.63 | −0.14 | 5.14 | 0.35 | 5.54 | −0.05 | 5.66 | −0.17 |
24 | 5.49 | 5.44 | 0.05 | 5.52 | −0.03 | 5.39 | 0.10 | 5.62 | −0.13 |
25 * | 5.32 | 5.60 | −0.28 | 5.56 | −0.24 | 5.85 | −0.53 | 5.88 | −0.56 |
26 | 5.21 | 5.39 | −0.18 | 5.39 | −0.18 | 5.11 | 0.10 | 4.87 | 0.34 |
27 * | 5.21 | 4.49 | 0.72 | 4.99 | 0.22 | 4.64 | 0.57 | 4.26 | 0.95 |
28 | 4.11 | 4.54 | −0.43 | 4.80 | −0.69 | 4.23 | −0.12 | 4.31 | −0.20 |
29 | 4.00 | 4.21 | −0.21 | 4.47 | −0.47 | 3.98 | 0.02 | 3.99 | 0.01 |
30 * | 4.00 | 3.90 | 0.10 | 4.07 | −0.07 | 3.91 | 0.09 | 4.18 | −0.18 |
31 | 4.00 | 3.89 | 0.11 | 3.99 | 0.01 | 4.03 | −0.03 | 3.81 | 0.19 |
32 | 4.00 | 4.08 | −0.08 | 3.95 | 0.05 | 3.98 | 0.02 | 3.95 | 0.05 |
33 | 4.00 | 3.85 | 0.15 | 4.17 | −0.17 | 3.94 | 0.06 | 4.06 | −0.06 |
34 | 4.00 | 3.95 | 0.05 | 3.79 | 0.21 | 4.04 | −0.04 | 4.23 | −0.23 |
35 | 4.00 | 3.98 | 0.02 | 3.79 | 0.21 | 3.96 | 0.04 | 3.82 | 0.18 |
36 * | 4.00 | 3.95 | 0.05 | 3.96 | 0.04 | 3.80 | 0.20 | 4.55 | −0.55 |
37 | 4.00 | 4.01 | −0.01 | 3.87 | 0.13 | 4.06 | −0.06 | 4.08 | −0.08 |
Training Set (%) | Score | r2 | SD | q2 | RMSE | N | Fingerprint |
---|---|---|---|---|---|---|---|
70 | 0.85 | 0.85 | 0.40 | 0.82 | 0.37 | 2 | Desc |
72 | 0.90 | 0.89 | 0.32 | 0.90 | 0.29 | 2 | Dendritic |
74 | 0.82 | 0.82 | 0.44 | 0.78 | 0.39 | 2 | Desc |
76 | 0.81 | 0.81 | 0.43 | 0.78 | 0.40 | 2 | Desc |
78 | 0.81 | 0.81 | 0.43 | 0.78 | 0.40 | 2 | Desc |
80 | 0.82 | 0.82 | 0.43 | 0.91 | 0.26 | 2 | Desc |
Model | q2 | r2 | r2pred | SEE | N | F | S | E | H | D | A |
---|---|---|---|---|---|---|---|---|---|---|---|
CoMFA | 0.72 | 0.99 | 0.81 | 0.08 | 6 | 595.85 | 0.41 | 0.59 | - | - | - |
CoMSIA | 0.63 | 0.96 | 0.73 | 0.21 | 3 | 179.60 | 0.11 | 0.34 | 0.17 | 0.14 | 0.24 |
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Medeiros, A.R.; Ferreira, L.L.G.; de Souza, M.L.; de Oliveira Rezende Junior, C.; Espinoza-Chávez, R.M.; Dias, L.C.; Andricopulo, A.D. Chemoinformatics Studies on a Series of Imidazoles as Cruzain Inhibitors. Biomolecules 2021, 11, 579. https://doi.org/10.3390/biom11040579
Medeiros AR, Ferreira LLG, de Souza ML, de Oliveira Rezende Junior C, Espinoza-Chávez RM, Dias LC, Andricopulo AD. Chemoinformatics Studies on a Series of Imidazoles as Cruzain Inhibitors. Biomolecules. 2021; 11(4):579. https://doi.org/10.3390/biom11040579
Chicago/Turabian StyleMedeiros, Alex R., Leonardo L. G. Ferreira, Mariana L. de Souza, Celso de Oliveira Rezende Junior, Rocío Marisol Espinoza-Chávez, Luiz Carlos Dias, and Adriano D. Andricopulo. 2021. "Chemoinformatics Studies on a Series of Imidazoles as Cruzain Inhibitors" Biomolecules 11, no. 4: 579. https://doi.org/10.3390/biom11040579
APA StyleMedeiros, A. R., Ferreira, L. L. G., de Souza, M. L., de Oliveira Rezende Junior, C., Espinoza-Chávez, R. M., Dias, L. C., & Andricopulo, A. D. (2021). Chemoinformatics Studies on a Series of Imidazoles as Cruzain Inhibitors. Biomolecules, 11(4), 579. https://doi.org/10.3390/biom11040579