Synthesis, Crystal Structure, DFT Analysis and Docking Studies of a Novel Spiro Compound Effecting on EGR-1-Regulated Gene Expression
Abstract
:1. Introduction
2. Materials and Methods
2.1. Synthetic Procedures
2.2. Crystal Structure Determination
2.3. Nuclear Magnetic Resonance (NMR) Spectroscopy
2.4. High-Resolution Mass Spectrometry (HR/MS)
2.5. In Silico Docking
2.6. Density Functional Theory (DFT) Calculations
2.7. Cells and Cell Culture
2.8. TSLP Gene Promoter-Reporter Assay
2.9. Reverse Transcription-PCR (RT-PCR)
2.10. Quantitative Real-Time PCR (qPCR)
2.11. Electrophoretic Mobility Shift Assay (EMSA)
3. Results and Discussion
3.1. Synthesis
3.2. Crystal Structure of Spiro Compound 4
3.3. DFT Calculations of Compound 4
3.4. Effects on EGR-1-Regulated Gene Expression
3.5. In Silico Docking
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Empirical Formula | C36H26F6O4 |
---|---|
Formula weight | 636.57 |
Temperature | 223(2) K |
Wavelength | 0.71073 Å |
Crystal system | Triclinic |
Space group | P-1 |
Unit cell dimensions | a = 8.8669(5) Å b = 10.5298(8) Å c = 17.0135(11) Å α = 91.396(2)°. β = 90.490(2)°. γ = 109.235(2)°. |
Volume | 1499.14(17) Å3 |
Z | 2 |
Density (calculated) | 1.410 Mg/m3 |
Absorption coefficient | 0.116 mm−1 |
F(000) | 656 |
Crystal size | 0.226 × 0.204 × 0.056 mm3 |
Theta range for data collection | 2.049 to 28.2492°. |
Index ranges | −1–11 ≤ h ≤ 11, −14 ≤ k ≤ 14, −22 ≤ l ≤ 22 |
Reflections collected | 44768 |
Independent reflections | 7389 [R(int) = 0.0426] |
Completeness to theta = 25.242° | 99.9% |
Refinement method | Full-matrix least-squares on F2 |
Data/restraints/parameters | 7389/30/445 |
Goodness-of-fit on F2 | 1.036 |
Final R indices [I > 2sigma(I)] | R1 = 0.0548, wR2 = 0.1309 |
R indices (all data) | R1 = 0.0814, wR2 = 0.1481 |
Largest diff. peak and hole | 0.531 and −0.420 e·Å−3 |
D-H…A | d(D-H) | d(H…A) | d(D…A) | <(DHA) |
---|---|---|---|---|
C(12)-H(12)…O(3)#1 | 0.99 | 2.57 | 3.444(3) | 146.4 |
C(34)-H(34)…O(1)#2 | 0.94 | 2.53 | 3.413(3) | 157.4 |
C(25)-H(25)…O(1)#3 | 0.94 | 2.43 | 3.356(2) | 169.2 |
4 | 5 | |
---|---|---|
FMO | Energy/Hartree(Eh) | Energy/Hartree(Eh) |
3rd LUMO | 0.1022 | 0.1233 |
2nd LUMO | 0.1016 | 0.1163 |
1st LUMO | 0.0919 | 0.0648 |
1st HOMO | −0.1635 | −0.3183 |
2nd HOMO | −0.1994 | −0.3236 |
3rd HOMO | −0.2541 | −0.3369 |
1st ΔE | 0.2554 | 0.3831 |
2nd ΔE | 0.3010 | 0.4399 |
3rd ΔE | 0.3563 | 0.4602 |
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Shin, S.Y.; Jung, E.; Lee, Y.; Lee, H.-J.; Lee, H.; Yoo, J.; Ahn, S.; Koh, D. Synthesis, Crystal Structure, DFT Analysis and Docking Studies of a Novel Spiro Compound Effecting on EGR-1-Regulated Gene Expression. Crystals 2025, 15, 338. https://doi.org/10.3390/cryst15040338
Shin SY, Jung E, Lee Y, Lee H-J, Lee H, Yoo J, Ahn S, Koh D. Synthesis, Crystal Structure, DFT Analysis and Docking Studies of a Novel Spiro Compound Effecting on EGR-1-Regulated Gene Expression. Crystals. 2025; 15(4):338. https://doi.org/10.3390/cryst15040338
Chicago/Turabian StyleShin, Soon Young, Euitaek Jung, Youngshim Lee, Ha-Jin Lee, Hyeonhwa Lee, Jinju Yoo, Seunghyun Ahn, and Dongsoo Koh. 2025. "Synthesis, Crystal Structure, DFT Analysis and Docking Studies of a Novel Spiro Compound Effecting on EGR-1-Regulated Gene Expression" Crystals 15, no. 4: 338. https://doi.org/10.3390/cryst15040338
APA StyleShin, S. Y., Jung, E., Lee, Y., Lee, H.-J., Lee, H., Yoo, J., Ahn, S., & Koh, D. (2025). Synthesis, Crystal Structure, DFT Analysis and Docking Studies of a Novel Spiro Compound Effecting on EGR-1-Regulated Gene Expression. Crystals, 15(4), 338. https://doi.org/10.3390/cryst15040338