Small Molecules Identified by an In Silico Docking Screen Targeting Anaphase-Promoting Complex/Cyclosome Subunit 1 (APC1) Potentiate Paclitaxel-Induced Breast Cancer Cell Death
Abstract
:1. Introduction
2. Results
3. Discussion
4. Materials and Methods
4.1. Protein and Ligand Data
4.2. Molecular Visualization and Analysis
4.3. Chemical Format Conversion and Ligand Preparation
4.4. Docking Simulations
4.5. Culturing RPE-1 and MDA-MB-231 Cells and Exposing Them to Drugs/Small Molecules and FACS Analyses
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Chemical Name | Chemical Formula | Molecular Weight (Da) | Modeled Binding Energy (kcal/mol) | Compound Database ID (Catalog Number), Experimentally Referred to as “Name” |
---|---|---|---|---|
[(1,2,3,4-tetrahydronaphthalen-1-yl)carbamoyl]methyl 4-oxo-3,4-dihydrophthalazine-1-carboxylate | C21H19N3O4 | 377.39 | −6.3 | ZINC000005182504 (Z86108408) “408” |
N-[(2H-1,3-benzodioxol-5-yl)methyl]-2-(trifluoromethyl)quinazolin-4-amine | C17H12F3N3O2 | 347.29 | −6.3 | ZINC000014197366 (Z86226558) “558” |
N-[2-(1H-indol-3-yl)ethyl]-2-(trifluoromethyl)quinazolin-4-amine | C19H15F3N4 | 356.34 | −6.3 | ZINC000008038860 (Z86252734) “734” |
N-[(3-benzyl-1,2,4-oxadiazol-5-yl)methyl]-1-(3,4-difluorophenyl)-1H,4H,5H,6H-cyclopenta[c]pyrazole-3-carboxamide | C23H19F2N5O2 | 435.43 | −6.4 | ZINC000057991268 (Z872761164) “164” |
2-[(1-phenyl-1H-pyrazol-4-yl)sulfonyl]-1,2,3,4-tetrahydroisoquinoline | C18H17N3O2S | 339.41 | −6.0 | ZINC000069037288 (Z873176686) “686” |
Small-Molecule Molarity | Relative Fold Decrease in the Mean Value of Living RPE-1 Cells (%) at 3 Days in 0.02% DMSO | Relative Fold Decrease in the Mean Value of Living MDA-MB-231Cells (%) at 3 Days in 0.02% DMSO | Relative Fold Decrease in the Mean Value of Living MDA-MB-231 cells (%) at 5 Days in 10 nM Paclitaxel | Relative Fold Decrease in the Mean Value of Living MDA-MB-231 Cells (%) at 5 Days in 1 nM Eribulin |
---|---|---|---|---|
10 μM 408 | - | - | - | - |
10 μM 558 | 1.8% | - | 9.8% | - |
10 μM 734 | - | 12.8% | 14.4% | - |
10 μM 164 | 1.8% | - | - | - |
10 μM 686 | 2.2% | - | - | - |
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Schuyler, S.C.; Gupta, R.; Nguyen, T.T.B.; Weng, C.-Y.; Chen, H.-Y. Small Molecules Identified by an In Silico Docking Screen Targeting Anaphase-Promoting Complex/Cyclosome Subunit 1 (APC1) Potentiate Paclitaxel-Induced Breast Cancer Cell Death. Molecules 2025, 30, 895. https://doi.org/10.3390/molecules30040895
Schuyler SC, Gupta R, Nguyen TTB, Weng C-Y, Chen H-Y. Small Molecules Identified by an In Silico Docking Screen Targeting Anaphase-Promoting Complex/Cyclosome Subunit 1 (APC1) Potentiate Paclitaxel-Induced Breast Cancer Cell Death. Molecules. 2025; 30(4):895. https://doi.org/10.3390/molecules30040895
Chicago/Turabian StyleSchuyler, Scott C., Rythm Gupta, Tran Thi Bao Nguyen, Cheng-Ye Weng, and Hsin-Yu Chen. 2025. "Small Molecules Identified by an In Silico Docking Screen Targeting Anaphase-Promoting Complex/Cyclosome Subunit 1 (APC1) Potentiate Paclitaxel-Induced Breast Cancer Cell Death" Molecules 30, no. 4: 895. https://doi.org/10.3390/molecules30040895
APA StyleSchuyler, S. C., Gupta, R., Nguyen, T. T. B., Weng, C.-Y., & Chen, H.-Y. (2025). Small Molecules Identified by an In Silico Docking Screen Targeting Anaphase-Promoting Complex/Cyclosome Subunit 1 (APC1) Potentiate Paclitaxel-Induced Breast Cancer Cell Death. Molecules, 30(4), 895. https://doi.org/10.3390/molecules30040895