Study of Cytotoxicity of 3-Azabicyclo[3.1.0]hexanes and Cyclopropa[a]pyrrolizidines Spiro-Fused to Acenaphthylene-1(2H)-one and Aceanthrylene-1(2H)-one Fragments Against Tumor Cell Lines
Abstract
1. Introduction
2. Results and Discussion
2.1. Chemistry
2.2. Biology
2.3. Actine Cytoskeleton Changes
2.4. Inhibition of Cell Motility Evaluated by Scratch-Test
2.5. Mitochondrial Membrane Potential (∆Ψm) Changes
2.6. Molecular Docking
3. Materials and Methods
3.1. Chemistry
In Silico Analysis
3.2. Cell Culture and Culturing Conditions
3.3. Cell Proliferation Assay
3.4. Actin Cytoskeleton Staining
3.5. Evaluation of Cell Motility by Scratch Test
3.6. Investigation of the Mitochondrial Membrane Potential (∆Ψm) Changes Under Incubation Conditions with Synthesized Compounds
3.7. Molecular Docking
3.8. Statistical Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Compound | MW | nHBD | nHBA | Log P | nRotB | TPSA, Å2 | NViolation | Meet Lipinski Criteria | Meet Veber Criteria | |
---|---|---|---|---|---|---|---|---|---|---|
Lipinski | Veber | |||||||||
<500 | <5 | <10 | ≤5 | <10 | <140 | <1 | 0 | Yes/No | Yes/No | |
1c | 453.57 | 0 | 2 | 5.54 | 3 | 20.31 | 1 | 0 | Yes | Yes |
1e | 503.63 | 0 | 2 | 6.13 | 3 | 20.31 | 2 | 0 | No | Yes |
1f | 485.57 | 0 | 4 | 4.62 | 4 | 46.61 | 1 | 0 | Yes | Yes |
1h | 519.63 | 1 | 3 | 5.25 | 3 | 40.54 | 2 | 0 | No | Yes |
1i | 521.67 | 0 | 2 | 5.95 | 3 | 45.61 | 2 | 0 | No | Yes |
2b | 519.67 | 1 | 2 | 6.30 | 6 | 29.10 | 2 | 0 | No | Yes |
2c | 519.67 | 1 | 2 | 6.30 | 5 | 29.10 | 2 | 0 | No | Yes |
2d | 537.71 | 1 | 2 | 6.13 | 6 | 54.40 | 2 | 0 | No | Yes |
2f | 569.73 | 1 | 2 | 6.82 | 6 | 29.10 | 2 | 0 | No | Yes |
Compound | HIA, % | BBB | PPB, % | CYP_2D6 Inhibition | Solubility, mg/L | Carcinogenicity (Rat/Mouse) | Mutagenicity | hERG Inhibition |
---|---|---|---|---|---|---|---|---|
1c | 100 | 2.01 | 93,41 | inhibitor | 0.0036 | negative/negative | mutagen | low risk |
1e | 100 | 2.53 | 97.22 | inhibitor | 0.0005 | negative/negative | non-mutagen | low risk |
1f | 98.17 | 5.69 | 90.55 | inhibitor | 0.0224 | negative/negative | mutagen | low risk |
1h | 96.97 | 1.59 | 100 | inhibitor | 0.0010 | negative/negative | mutagen | low risk |
1i | 98.31 | 5.44 | 100 | inhibitor | 9 × 10−5 | negative/negative | non-mutagen | low risk |
2b | 97.18 | 10.22 | 100 | inhibitor | 4 × 10−5 | positive/negative | non-mutagen | low risk |
2c | 97.18 | 5.89 | 100 | inhibitor | 5 × 10−5 | negative/negative | mutagen | low risk |
2d | 97.64 | 0.36 | 100 | inhibitor | 0.0001 | negative/negative | non-mutagen | low risk |
2f | 96.85 | 9.74 | 100 | inhibitor | 7 × 10−7 | positive/negative | non-mutagen | low risk |
Compound | IC50, μM | Compound | IC50, μM | ||||
---|---|---|---|---|---|---|---|
K562 | U2OS | B16 | K562 | U2OS | B16 | ||
1a | >40 | >40 | 15 ± 3 | 1h | 12 ± 2 | 28 ± 7 | 4 ± 1 |
1b | 13 ± 2 | >40 | 10 ± 2 | 1i | >40 | >40 | 13 ± 4 |
1c | >40 | >40 | 11 ± 2 | 1j | >40 | >40 | 20 ± 5 |
1d | >40 | >40 | 15 ± 4 | 2b | 27 ± 5 | >40 | 22 ± 7 |
1e | >40 | >40 | 7 ± 2 | 2c | 25 ± 4 | >40 | >40 |
1f | 4 ± 1 | >40 | 7 ± 2 | Doxorubicin | 1 ± 0.3 | 7 ± 2 | 6 ± 1 |
1g | 17 ± 4 | >40 | 8 ± 2 |
# | Protein PDB ID | Ligand | MolDock Score a | Rerank Score a | HBond a | Amino Acid Residue ID (Target-Binding Cleft) b |
---|---|---|---|---|---|---|
1 | 8DNH | 1b | −153.95 | −97.868 | 0 | Ala 107, Arg 115, Asn 110, Cys 373, Glu 106, His 172, His 370, Ile 135, Ile 174, Leu 109, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Val 369, Glu 194, Lys 190, Thr 193 |
2 | 8DNH | 1c | −159.21 | −100.86 | 0 | Ala 107, Arg 115, Asn 110, Cys 373, Glu 106, His 172, His 370, Ile 135, Ile 174, Leu 109, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Val 369, Glu 194, Lys 190, Thr 193 |
3 | 8DNH | 1e | −160.79 | −101.22 | 0 | Arg 115, Arg 371, Asn 110, Glu 106, His 172, His 370, Ile 135, Ile 174, Leu 109, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Val 369, Glu 194, Lys 190, Thr 193 |
4 | 8DNH | 1f | −157.07 | −99.393 | −5.088 | Ala 107, Arg 115, Asn 110, Cys 373, Glu 106, His 172, His 370, Ile 135, Ile 174, Leu 109, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Val 369, Glu 194, Lys 190, Thr 193 |
5 | 8DNH | 1g | −152.95 | −98.533 | −1.274 | Ala 107, Arg 115, Asn 110, Glu 106, His 172, His 370, Ile 135, Ile 174, Leu 109, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Val 369, Glu 194, Lys 190, Thr 193 |
6 | 8DNH | 1i | −163.94 | −99.137 | 0 | Ala 107, Arg 115, Arg 371, Asn 110, Glu 106, His 172, His 370, Ile 135, Ile 174, Leu 109, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Val 369, Glu 194, Lys 190, Thr 193 |
7 | 8DNH | 2b | −177.53 | −105.71 | 0 | Ala 107, Arg 115, Arg 371, Asn 110, Cys 373, Glu 106, His 172, His 370, Ile 135, Ile 174, Leu 109, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Val 133, Val 369, Glu 194, Lys 190, Thr 193 |
8 | 8DNH | 2c | −172.68 | −93.067 | −2.874 | Ala 107, Ala 134, Ala 169, Arg 115, Asn 110, Cys 373, Glu 106, His 370, Ile 135, Ile 174, Leu 109, Leu 170, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Tyr 132, Val 133, Val 138, Val 162, Val 42 |
9 | 8DNH | 2d | −176.60 | −115.24 | −0.799 | Ala 107, Ala 134, Ala 169, Arg 115, Asn 110, Cys 373, Glu 106, His 370, Ile 135, Ile 174, Leu 109, Leu 170, Lys 112, Phe 374, Pro 108, Pro 111, Pro 171, Tyr 132, Val 133, Val 138, Val 162, Val 42 |
# | Protein PDB ID | Ligand | MolDock Score a | Rerank Score a | HBond a |
---|---|---|---|---|---|
1 | 7BJ6 | TVK* | −159.09 | −108.74 | −2.261 |
2 | 7BJ6 | 1b | −142.49 | −88.908 | 0 |
3 | 7BJ6 | 1c | −134.28 | −83.325 | 0 |
4 | 7BJ6 | 1e | −138.17 | −77.631 | 0 |
5 | 7BJ6 | 1f | −132.48 | −77.205 | 0 |
6 | 7BJ6 | 1g | −130.21 | −76.526 | 0 |
7 | 7BJ6 | 1i | −135.84 | −76.857 | 0 |
8 | 7BJ6 | 2b | −159.08 | −97.295 | −0.764 |
9 | 7BJ6 | 2c | −148.45 | −74.777 | 0 |
10 | 7BJ6 | 2d | −158.34 | −85.999 | 0 |
11 | 7BJ6 | TUZ | −163.89 | −111.47 | −2.918 |
12 | 7BIR | TUZ* | −166.93 | −112.48 | −3.878 |
13 | 7BIR | 1b | −139.12 | −85.431 | 0 |
14 | 7BIR | 1c | −135.18 | −81.189 | 0 |
15 | 7BIR | 1e | −138.72 | −72.773 | 0 |
16 | 7BIR | 1f | −134.55 | −69.128 | 0 |
17 | 7BIR | 1g | −137.06 | −82.389 | 0 |
18 | 7BIR | 1i | −136.86 | −68.419 | 0 |
19 | 7BIR | 2b | −158.62 | −96.458 | 0 |
20 | 7BIR | 2c | −151.68 | −81.008 | 0 |
21 | 7BIR | 2d | −162.68 | −94.685 | 0 |
22 | 7BIR | TVK | −145.61 | −96.633 | −5.341 |
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Kornev, A.A.; Shmakov, S.V.; Gryschenko, A.M.; Pronina, Y.A.; Ponyaev, A.I.; Stepakov, A.V.; Boitsov, V.M. Study of Cytotoxicity of 3-Azabicyclo[3.1.0]hexanes and Cyclopropa[a]pyrrolizidines Spiro-Fused to Acenaphthylene-1(2H)-one and Aceanthrylene-1(2H)-one Fragments Against Tumor Cell Lines. Int. J. Mol. Sci. 2025, 26, 3474. https://doi.org/10.3390/ijms26083474
Kornev AA, Shmakov SV, Gryschenko AM, Pronina YA, Ponyaev AI, Stepakov AV, Boitsov VM. Study of Cytotoxicity of 3-Azabicyclo[3.1.0]hexanes and Cyclopropa[a]pyrrolizidines Spiro-Fused to Acenaphthylene-1(2H)-one and Aceanthrylene-1(2H)-one Fragments Against Tumor Cell Lines. International Journal of Molecular Sciences. 2025; 26(8):3474. https://doi.org/10.3390/ijms26083474
Chicago/Turabian StyleKornev, Anton A., Stanislav V. Shmakov, Alexandra M. Gryschenko, Yulia A. Pronina, Alexander I. Ponyaev, Alexander V. Stepakov, and Vitali M. Boitsov. 2025. "Study of Cytotoxicity of 3-Azabicyclo[3.1.0]hexanes and Cyclopropa[a]pyrrolizidines Spiro-Fused to Acenaphthylene-1(2H)-one and Aceanthrylene-1(2H)-one Fragments Against Tumor Cell Lines" International Journal of Molecular Sciences 26, no. 8: 3474. https://doi.org/10.3390/ijms26083474
APA StyleKornev, A. A., Shmakov, S. V., Gryschenko, A. M., Pronina, Y. A., Ponyaev, A. I., Stepakov, A. V., & Boitsov, V. M. (2025). Study of Cytotoxicity of 3-Azabicyclo[3.1.0]hexanes and Cyclopropa[a]pyrrolizidines Spiro-Fused to Acenaphthylene-1(2H)-one and Aceanthrylene-1(2H)-one Fragments Against Tumor Cell Lines. International Journal of Molecular Sciences, 26(8), 3474. https://doi.org/10.3390/ijms26083474