Fragment-Based Discovery of AF9 YEATS Domain Inhibitors
Abstract
:1. Introduction
2. Results
3. Conclusions
4. Materials and Methods
4.1. Cloning, Protein Expression, and Purification
4.2. Ligand-Observed Fragment Screening
4.3. NMR Chemical Shift Perturbation
4.4. Isothermal Titration Calorimetry
4.5. Crystallization, Data collection
4.6. Structure Determination and Refinement
4.7. Cell Viability Assay
4.8. Chemical Synthesis and Characterization
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
YEATS | YAF9, ENL, AF9, TAF14, SAS5 |
STD | Saturation Transfer Difference |
CPMG | Carr–Purcell–Meiboom–Gill |
CSPs | Chemical shift perturbations |
HSQC | Heteronuclear single-quantum coherence |
NMR | Nuclear Magnetic Resonance |
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ID | Structure | Kd (mM) a | LE | ID | Structure | Kd (mM) | LE |
---|---|---|---|---|---|---|---|
1 | | 0.137 ± 0.024 b | 0.38 | 8 | | 0.31 ± 0.004 | 0.36 |
2 | | 0.07 ± 0.01 | 0.41 | 9 | | 0.66 ± 0.07 | 0.26 |
3 | | 0.10 ± 0.01 | 0.39 | 10 | | 0.038 ± 0.006 | 0.42 |
4 | | 0.44 ± 0.10 | 0.33 | 11 | | 0.088 ± 0.03 | 0.31 |
5 | | 0.08 ± 0.06 | 0.43 | 12 | | 0.087 ± 0.011 | 0.28 |
6 | | 0.061 ± 0.004 | 0.41 | 13 | | 0.07 ± 0.009 | 0.28 |
7 | | 0.27 ± 0.02 | 0.29 | 14 | | 0.026 ± 0.004 | 0.30 |
PDB ID | 7VKH | 7VKG |
---|---|---|
Data Collection | ||
Space group | P1 | P21 |
Cell dimensions | ||
a, b, c (Å) | 31.652, 41.426, 59.725 | 41.381, 31.553, 89.378 |
α, β, γ (°) | 102, 90.87, 90.357 | 90, 102.04, 90 |
Wavelength (Å) | 0.9774 | 0.9785 |
Resolution (Å) | 40.00–2.25 (2.29–2.25) * | 40.00–1.83 (1.86–1.83) * |
Completeness (%) | 97.6 (93.6) | 99.1 (97.4) |
Redundancy | 3.3 (2.5) | 6.6 (5.9) |
Rsym or Rmerge (%) | 11.1 (38.1) | 7.9 (65.2) |
I/σI | 9.26 (2.05) | 20.44 (2.67) |
Refinement | ||
No. reflections used/free | 13,767/703 | 13,843/649 |
Rwork/Rfree (%) | 20.61/24.45 | 20.20/24.54 |
R.m.s.deviations | ||
Bond lengths (Å) | 0.003 | 0.004 |
Bond angles (°) | 0.669 | 0.767 |
B-factors (Å2) | ||
Protein | 28.08 | 26.00 |
Ligand | 33.16 | 31.26 |
Water | 26.91 | 32.43 |
No. atoms | ||
Protein | 2228 | 1116 |
Ligand | 28 | 19 |
Water | 35 | 61 |
Ramachandran plot | ||
Favored/allowed/outlier (%) | 98.87/1.13/0 | 100/0/0 |
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Liu, Y.; Jin, R.; Lu, H.; Bian, K.; Wang, R.; Wang, L.; Gao, R.; Zhang, J.; Wu, J.; Yao, X.; et al. Fragment-Based Discovery of AF9 YEATS Domain Inhibitors. Int. J. Mol. Sci. 2022, 23, 3893. https://doi.org/10.3390/ijms23073893
Liu Y, Jin R, Lu H, Bian K, Wang R, Wang L, Gao R, Zhang J, Wu J, Yao X, et al. Fragment-Based Discovery of AF9 YEATS Domain Inhibitors. International Journal of Molecular Sciences. 2022; 23(7):3893. https://doi.org/10.3390/ijms23073893
Chicago/Turabian StyleLiu, Yaqian, Ruoxing Jin, Hui Lu, Kangjie Bian, Rui Wang, Lei Wang, Rui Gao, Jiahai Zhang, Jihui Wu, Xuebiao Yao, and et al. 2022. "Fragment-Based Discovery of AF9 YEATS Domain Inhibitors" International Journal of Molecular Sciences 23, no. 7: 3893. https://doi.org/10.3390/ijms23073893
APA StyleLiu, Y., Jin, R., Lu, H., Bian, K., Wang, R., Wang, L., Gao, R., Zhang, J., Wu, J., Yao, X., Liu, X., Liu, D., Wang, X., Zhang, Z., & Ruan, K. (2022). Fragment-Based Discovery of AF9 YEATS Domain Inhibitors. International Journal of Molecular Sciences, 23(7), 3893. https://doi.org/10.3390/ijms23073893