Synthesis, Docking, and Machine Learning Studies of Some Novel Quinolinesulfonamides–Triazole Hybrids with Anticancer Activity
Abstract
:1. Introduction
2. Results and Discussion
2.1. Design and In Silico Prediction of ROCK1 Inhibitors
2.1.1. Machine Learning
2.1.2. Molecular Docking
2.1.3. Molecular Dynamics Calculations
2.1.4. Prediction of Drug-likeness and ADMET Profile of Designed Compounds
2.2. Chemistry
- (i)
- 8-quinolinesulfochloride 1 (1 eq), conc. NH4OH, 45 °C, 0.5 h;
- (ii)
- 8-quinolinesulfonamide 2 (1 eq), KOH (1.5 eq), propargyl alcohol, b.p, 6 h;
- (iii)
- 8-(N-propargyl)quinolinesulfonamide 3a (1 eq), CH3I (1.1 eq), 5% NaOH, r.t., over night;
- (iv)
- Procedure A: 8-quinolinesulfonamide 3a or 3b (1 eq), organic azide (1.1. eq), CuSO4 × 5 H2O, sodium acorbate, DMF/H2O, ambient terperatur, over night; Procedure B: organic bromide (1 eq), NaN3 (1.2 eq), DMF, ambient terperatur, over night and then 8-quinolinesulfonamide (1 eq), CuSO4 × 5 H2O, sodium acorbate, DMF/H2O, ambient terperatur, over night.
2.3. In Vitro Studies
3. Materials and Methods
3.1. In Silico
3.2. Chemistry
3.2.1. General Chemistry Methods
3.2.2. Synthesis of Quinolinesulfonamide 2
3.2.3. Synthesis of Quinolinesulfonamide 3a
3.2.4. Synthesis of Quinolinesulfonamide 3b
3.2.5. Synthesis of Triazoles 4–14
3.3. In Vitro Studies
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Compound | Edock-ML | Vina ∆G [kcal/mol] | ||
---|---|---|---|---|
Sensitivity | Specificity | AUC Value | ||
4a | 0.9 | 0.77 | 0.82 | −9.2 |
4b | 0.9 | 0.71 | 0.82 | −9.3 |
5a | 0.9 | 0.9 | 0.82 | −9.7 |
5b | 0.9 | 0.64 | 0.82 | −9.4 |
6a | 0.9 | 0.71 | 0.82 | −9.5 |
6b | 0.9 | 0.64 | 0.82 | −9.6 |
7a | 0.9 | 0.56 | 0.82 | −9.4 |
7b | 0.9 | 0.56 | 0.82 | −9.2 |
8a | 0.9 | 0.9 | 0.82 | −9.1 |
8b | 0.9 | 0.64 | 0.82 | −9.1 |
9a | 0.9 | 0.9 | 0.82 | −9.7 |
9b | 0.9 | 0.9 | 0.82 | −10.4 |
10a | 0.9 | 0.71 | 0.82 | −10.3 |
10b | 0.9 | 0.77 | 0.82 | −10.0 |
11a | 0.9 | 0.9 | 0.82 | −9.9 |
11b | 0.9 | 0.56 | 0.82 | −9.7 |
12a | 0.9 | 0.71 | 0.82 | −7.9 |
12b | 0.9 | 0.56 | 0.82 | −8.2 |
13a | 0.9 | 0.64 | 0.82 | −8.1 |
13b | 0.9 | 0.64 | 0.82 | −8.2 |
14a | 0.9 | 0.64 | 0.82 | −9.7 |
14b | 0.9 | 0.9 | 0.82 | −9.7 |
Fasudil | 0.9 | 0.71 | 0.82 | −7.9 |
Protein | Ligand | Interaction | |||
---|---|---|---|---|---|
Name | Residue | Name | Residue | Type | Distance [Å] |
ROCK1 | Asn203 Asp216 Arg84 Ile82 Lys105 Asp216 Asp216 Val90 Leu205 Phe120 Ala103 Val90 Met153 Ala103 Met153 Ala215 Val90 Val90 Leu205 | 9b | methylene group methylene group methyl group pyridine ring benzene ring triazole ring benzene ring benzene ring benzene ring pyridine ring chlorine atom chlorine atom chlorine atom benzene ring benzene ring benzene ring triazole ring pyridine ring pyridine ring | carbon–hydrogen bond carbon–hydrogen bond carbon–hydrogen bond carbon–hydrogen bond π–cation π–anion π–anion π–sigma π–sigma π–sigma π–π, T-shaped alkyl alkyl π–alkyl π–alkyl π–alkyl π–alkyl π–alkyl π–alkyl | 2.76 3.03 2.83 2.25 4.29 3.29 3.66 3.93 3.77 5.31 3.00 4.59 3.22 5.06 5.47 4.61 5.39 4.19 5.29 |
Gly85 Ile82 Lys105 Asp216 Asp216 Asp216 Val90 Leu205 Met153 Phe120 Ala103 Ile82 Leu205 Tyr155 Phe368 Val90 Val90 Leu205 Ala103 Ala215 | 10a | sulfonamide group pyridine ring benzene ring benzene ring pyridine ring triazole ring benzene ring benzene ring benzene ring pyridine ring benzene ring bromine atom bromine atom bromine atom bromine atom pyridine ring triazole ring pyridine ring bromine atom benzene ring | carbon–hydrogen bond carbon–hydrogen bond π–cation π–anion π–anion π–anion π–sigma π–sigma π–sulphur π–π, T-shaped alkyl alkyl alkyl π–alkyl π–alkyl π–alkyl π–alkyl π–alkyl π–alkyl π–alkyl | 3.52 3.23 3.31 3.31 4.19 4.76 3.79 3.84 5.32 5.34 3.68 5.16 5.15 5.08 5.03 5.42 4.54 5.15 5.13 4.80 | |
Asn203 Arg84 Ile82 Lys105 Asp216 Asp216 Val90 Leu205 Met153 Phe120 Ala103 Ile82 Leu205 Tyr155 Phe368 Val90 Leu205 Ala103 Ala215 | 10b | methylene group methyl group pyridine ring benzene ring benzene ring triazole ring benzene ring benzene ring benzene ring pyridine ring benzene ring bromine atom bromine atom bromine atom bromine atom benzene ring pyridine ring bromine atom benzene ring | carbon–hydrogen bond carbon–hydrogen bond carbon–hydrogen bond π–cation π–anion π–anion π–sigma π–sigma π–sulphur π–π, T-shaped alkyl alkyl alkyl π–alkyl π–alkyl π–alkyl π–alkyl π–alkyl π–alkyl | 3.60 3.61 3.23 4.38 3.32 3.81 3.85 3.81 5.34 5.15 3.62 5.14 5.20 5.09 5.07 4.58 5.12 5.19 4.75 |
Comp. | Physicochemical Properties | |||||||
---|---|---|---|---|---|---|---|---|
MW | nROT | nHBA | nHBD | MR | TPSA | MLOGP | WLOGP | |
4a | 379.44 | 6 | 6 | 1 | 101.45 | 98.15 | 1.52 | 3.28 |
4b | 393.46 | 6 | 6 | 0 | 106.36 | 89.36 | 1.75 | 3.62 |
5a | 404.45 | 6 | 7 | 1 | 106.17 | 121.94 | 0.89 | 3.15 |
5b | 418.47 | 6 | 7 | 0 | 111.07 | 113.15 | 1.11 | 3.50 |
6a | 397.43 | 6 | 7 | 1 | 101.41 | 98.15 | 1.90 | 3.84 |
6b | 411.45 | 6 | 7 | 0 | 106.31 | 89.36 | 2.13 | 4.18 |
7a | 424.43 | 7 | 8 | 1 | 110.28 | 143.97 | 0.67 | 3.19 |
7b | 438.46 | 7 | 8 | 0 | 115.18 | 135.18 | 0.89 | 3.53 |
8a | 411.50 | 7 | 6 | 1 | 108.21 | 123.45 | 1.79 | 3.83 |
8b | 425.53 | 7 | 6 | 0 | 113.11 | 114.66 | 2.01 | 4.17 |
9a | 450.90 | 5 | 7 | 1 | 117.35 | 111.04 | 2.03 | 4.42 |
9b | 464.93 | 5 | 7 | 0 | 122.25 | 102.25 | 2.25 | 4.77 |
10a | 495.35 | 5 | 7 | 1 | 120.04 | 111.04 | 2.14 | 4.53 |
10b | 509.38 | 5 | 7 | 0 | 124.94 | 102.25 | 2.35 | 4.88 |
11a | 513.53 | 7 | 10 | 3 | 126.96 | 182.47 | −0.93 | 0.59 |
11b | 527.55 | 7 | 10 | 2 | 131.86 | 173.68 | −0.71 | 0.93 |
12a | 345.42 | 7 | 6 | 1 | 91.39 | 98.15 | 1.02 | 3.03 |
12b | 395.45 | 7 | 6 | 0 | 96.29 | 89.36 | 1.26 | 3.38 |
13a | 389.43 | 9 | 8 | 1 | 97.48 | 124.45 | 0.44 | 2.19 |
13b | 403.46 | 9 | 8 | 0 | 102.38 | 115.66 | 0.67 | 2.53 |
14a | 814.09 | 12 | 10 | 1 | 225.82 | 150.75 | 5.14 | 9.37 |
14b | 828.11 | 12 | 10 | 0 | 230.73 | 141.96 | 5.30 | 9.71 |
Lipinski’s Rule (MW ≤ 500; MLOGP ≤ 4.15; nHBA ≤ 10; nHBD ≤ 5) | Ghose’s Rule (160 ≤ MW ≤ 480; 40 ≤ MR ≤ 130 −0.4 ≤ WLOG ≤ 5.6; 20 ≤ Atoms ≤ 70 | Veber’s Rule (nROT ≤ 10; TPSA ≤ 140 Å2) | |||||||
---|---|---|---|---|---|---|---|---|---|
Drug- Likeness | Number and Type of Violations | Drug- Likeness | Number and Type of Violations | Drug- Likeness | Number and Type of Violations | ||||
7a | Yes | 0 | - | Yes | 0 | - | No | 1 | TPSA |
10a | Yes | 0 | - | No | 1 | MW | Yes | 0 | - |
10b | Yes | 1 | MW | No | 1 | MW | Yes | 0 | - |
11a | Yes | 1 | MW | No | 1 | MW | No | 1 | TPSA |
11b | Yes | 1 | MW | No | 2 | MW MR | No | 1 | TPSA |
14a | No | 2 | MW MLOGP | No | 4 | MW WLOGP MR #atoms | No | 2 | nROT TPSA |
14b | No | 2 | MW MLOGP | No | 4 | MW WLOGP MR #atoms | No | 2 | nROT TPSA |
Absorption | Distribution | Metabolism | Tox. | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
LogS (ESOL) * | Caco2 Perm. | HIA | P-gp Sub. | BBB Perm. | CNS Perm. | CYP1A2 Inh. | CYP3A4 Inh. | CYP2C19 Inh. | CYP2D6 Inh. | Ames | |
4a | −3.66 | 0.948 | 96.972 | yes | −0.942 | −2.617 | yes | yes | yes | no | no |
4b | −3.84 | 0.917 | 99.431 | no | −1.108 | −2.486 | yes | yes | yes | no | yes |
5a | −3.60 | 0.24 | 92.754 | yes | −1.11 | −2.684 | yes | yes | yes | no | no |
5b | −3.79 | 0.926 | 94.5 | no | −1.276 | −2.553 | no | yes | yes | no | yes |
6a | −3.82 | 1.104 | 96.47 | yes | −1.162 | −3.195 | yes | yes | yes | no | no |
6b | −4.00 | 1.072 | 98.929 | no | −1.328 | −3.092 | no | yes | yes | no | yes |
7a | −3.71 | −0.199 | 91.898 | yes | −1.457 | −2.844 | no | yes | yes | no | yes |
7b | −3.90 | 0.326 | 93.644 | yes | −1.623 | −2.712 | no | yes | yes | no | yes |
8a | −4.18 | 0.888 | 95.224 | yes | −1.123 | −2.592 | yes | yes | yes | no | no |
8b | −4.36 | 0.903 | 97.683 | no | −1.29 | −2.461 | yes | yes | yes | no | yes |
9a | −4.80 | 0.644 | 95.149 | yes | −1.412 | −3.045 | no | yes | no | no | no |
9b | −4.98 | 0.34 | 99.063 | no | −1.579 | −2.953 | yes | yes | no | no | no |
10a | −5.11 | 0.66 | 94.835 | yes | −1.415 | −3.03 | no | yes | no | no | no |
10b | −5.29 | 0.341 | 99.552 | no | −1.582 | −2.927 | no | yes | no | no | no |
11a | −2.56 | −0.08 | 79.864 | yes | −2.137 | −4.205 | no | no | no | no | no |
11b | −2.75 | −0.073 | 84.581 | yes | −2.178 | −4.102 | no | yes | no | no | no |
12a | −3.02 | 0.92 | 96.028 | yes | −0.94 | −2.875 | no | yes | yes | no | no |
12b | −3.20 | 0.877 | 98.599 | no | −1.107 | −2.743 | yes | yes | yes | no | no |
13a | −2.44 | 0.577 | 84.401 | yes | −1.375 | −3.651 | no | no | no | no | no |
13b | −2.62 | 0.68 | 89.118 | no | −1.542 | −3.548 | yes | yes | no | no | no |
14a | −9.69 | 0.047 | 100 | yes | −1.599 | −2.789 | no | yes | no | no | no |
14b | −10.08 | 0.327 | 100 | yes | −1.766 | −2.686 | no | yes | no | no | no |
Compound | IC50 [µM] | ||||
---|---|---|---|---|---|
Caco-2 | SNB-19 | A-549 | SKOV-3 | NHDF | |
4a | 26.38 | neg | neg | neg | neg |
4b | 0.40 | 1.18 | 7.72 | 66.16 | 190.81 |
5a | 2.21 | neg | neg | neg | neg |
5b | 0.40 | 0.41 | 0.80 | 14.06 | 9.16 |
6a | 27.51 | neg | neg | neg | neg |
6b | 19.33 | 156.22 | neg | neg | neg |
7a | 0.31 | 0.83 | 36.11 | 16.92 | 169.33 |
7b | 2.47 | 0.41 | neg | neg | neg |
8a | 14.29 | 72.39 | 3.69 | 114.81 | 40.58 |
8b | 0.34 | 0.35 | neg | neg | neg |
9a | 17.98 | 62.42 | neg * | 107.86 | neg |
9b | 0.26 | 0.38 | 0.40 | 4.16 | neg |
10a | 9.69 | 37.36 | 113.37 | 94.49 | neg |
10b | 0.30 | 0.30 | 1.77 | 24.73 | 26.19 |
11a | 0.36 | 128.89 | 18.05 | 143.34 | 194.93 |
11b | 0.48 | 0.59 | 1.29 | 7.16 | 98.28 |
12a | 0.38 | 0.44 | neg * | 53.86 | neg |
12b | 1.29 | 63.57 | 188.65 | 80.37 | 242.26 |
13a | 0,32 | 0.39 | neg * | 64.56 | 222.61 |
13b | 85.19 | 137.93 | neg | 88.17 | neg |
14a | neg | 101.48 | neg | neg | neg |
14b | 18.2 | 9.26 | neg * | 1.09 | neg |
Cisplatin | 0.27 | 2.93 | 453.41 | 41.65 | neg |
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Marciniec, K.; Nowakowska, J.; Chrobak, E.; Bębenek, E.; Latocha, M. Synthesis, Docking, and Machine Learning Studies of Some Novel Quinolinesulfonamides–Triazole Hybrids with Anticancer Activity. Molecules 2024, 29, 3158. https://doi.org/10.3390/molecules29133158
Marciniec K, Nowakowska J, Chrobak E, Bębenek E, Latocha M. Synthesis, Docking, and Machine Learning Studies of Some Novel Quinolinesulfonamides–Triazole Hybrids with Anticancer Activity. Molecules. 2024; 29(13):3158. https://doi.org/10.3390/molecules29133158
Chicago/Turabian StyleMarciniec, Krzysztof, Justyna Nowakowska, Elwira Chrobak, Ewa Bębenek, and Małgorzata Latocha. 2024. "Synthesis, Docking, and Machine Learning Studies of Some Novel Quinolinesulfonamides–Triazole Hybrids with Anticancer Activity" Molecules 29, no. 13: 3158. https://doi.org/10.3390/molecules29133158
APA StyleMarciniec, K., Nowakowska, J., Chrobak, E., Bębenek, E., & Latocha, M. (2024). Synthesis, Docking, and Machine Learning Studies of Some Novel Quinolinesulfonamides–Triazole Hybrids with Anticancer Activity. Molecules, 29(13), 3158. https://doi.org/10.3390/molecules29133158