Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC
Abstract
:1. Introduction
2. Results
2.1. New Piperidine Analogs
2.2. The Design and Synthesis of New CD4mc Piperidine Analogs
2.3. Biological Testing
2.4. Structural Basis of Interaction of (S)-MCG-IV-210 Derivatives with a gp120 Core
2.5. (S)-MCG-IV-210 Derivatives Inhibit Viral Infection
2.6. Sensitization of HIV-1-Infected Cells to ADCC
2.7. BLI Competition Assay
3. Discussion
4. Materials and Methods
4.1. Ethics Statement
4.2. Cell Lines and Isolation of Primary Cells
4.3. Chemical Synthesis: General Considerations
4.4. Viral Production and Infection of Primary CD4+ T Cells
4.5. Viral Neutralization
4.6. Antibodies and Plasma
4.7. Flow Cytometry Analysis of Cell-Surface Staining
4.8. Cell Viability Test
4.9. ADCC FACS-Based Assay
4.10. Statistical Analysis
4.11. CRF01_AE Core e Expression and Purification
4.12. Biolayer Interferometry (BLI) Competition Assay
4.13. Crystallization of gp120 Cores Complex with CD4mc
4.14. Data Collection, Structure Solution and Refinement
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Disclaimer
References
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LM/HT gp120CRF01_AE Coree—TFH-I-070-A6 | LM/HT gp120CRF01_AE Coree—TFH-I-116-D1 | LM/HT gp120CRF01_AE Coree—ZXC-I-090 | LM/HT gp120CRF01_AE Coree—ZXC-I-092 | LM/HS gp120CRF01_AE Coree—DL-I-101 | LM/HS gp120CRF01_AE Coree—DL-I-102 | |
---|---|---|---|---|---|---|
Data collection | ||||||
Wavelength, Ǻ | 0.979 | 0.979 | 0.979 | 0.979 | 0.979 | 0.979 |
Space group | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 |
Cell parameters | ||||||
a, b, c, Å | 63.6, 66.3, 91.4 | 64.7, 66.0, 87.8 | 61.8, 65.9, 91.2 | 60.0, 65.2, 87.3 | 67.7, 66.9, 92.2 | 194.5, 86.6, 57.7 |
α, β, γ, ° | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 909, 90 | 90, 90, 90 | 90, 90, 90 |
Molecules/a.u. | 1 | 1 | 1 | 1 | 1 | 1 |
Resolution, (Å) | 50–2.4 (2.44–2.4) | 50–3.5 (3.69–3.5) | 50–2.4 (2.44–2.4) | 50–2.85 (2.9–2.85) | 50–2.19 (2.23–2.19) | 50–2.6 (2.64–2.6) |
# of reflections | ||||||
Total | 49,666 | 11,650 | 61,106 | 34,488 | 86,920 | 39,768 |
Unique | 13,796 | 4021 | 14,904 | 7185 | 20,214 | 10,748 |
Rmerge a, % | 9.1 (57.9) | 22.3 (113) | 10.6 (80.1) | 12.1 (104) | 17.2 (66.5) | 15.4 (98.3) |
Rpim b, % | 5.1 (32.3) | 14.7 (72.9) | 5.8 (71.1) | 8.2 (77.4) | 9.7 (36.4) | 9.0 (65.0) |
CC1/2 c | 0.98 (0.71) | 0.97 (0.33) | 1.0 (0.50) | 1.0 (0.42) | 1.0 (0.65) | 0.94 (0.60) |
I/σ | 12.3 (1.3) | 2.8 (0.6) | 14.2 (0.8) | 12.5 (0.8) | 25.5 (2.1) | 17.3 (1.1) |
Completeness, % | 88.3 (78.2) | 80.6 (83.9) | 97.8 (86.4) | 83.3 (78.0) | 97.4 (85.0) | 86.1 (90.2) |
Redundancy | 3.6 (3.7) | 2.9 (3.0) | 4.1 (2.7) | 4.8 (4.2) | 4.3 (3.8) | 3.7 (3.1) |
Refinement Statistics | ||||||
Resolution, Å | 50.0–2.4 | 50.0–3.5 | 50.0–2.4 | 50.0–2.85 | 50.0–2.19 | 50.0–2.6 |
R d % | 22.1 | 25.6 | 24.0 | 24.2 | 20.8 | 22.1 |
Rfree e, % | 27.4 | 30.7 | 26.7 | 29.6 | 25.5 | 27.4 |
# of atoms | ||||||
Protein | 2,668 | 2,640 | 2,665 | 2,675 | 2,683 | 2,668 |
Water | 32 | – | 23 | – | 64 | 2 |
Ligand/Ion | 212 | 184 | 211 | 186 | 193 | 186 |
Overall B value (Å)2 | ||||||
Protein | 52 | 82 | 62 | 73 | 53 | 85 |
Water | 48 | – | 56 | – | 49 | 74 |
Ligand/Ion | 70 | 96 | 74 | 86 | 63 | 102 |
RMSD f | ||||||
Bond lengths, Å | 0.005 | 0.004 | 0.006 | 0.009 | 0.007 | 0.012 |
Bond angles, ° | 1.0 | 0.79 | 0.98 | 1.3 | 1.0 | 1.4 |
Ramachandran g | ||||||
Favored, % | 94.0 | 90.2 | 94.0 | 89.5 | 95.0 | 92.5 |
Allowed, % | 4.2 | 7.4 | 5.4 | 9.0 | 4.7 | 7.2 |
Outliers, % | 1.8 | 2.4 | 0.6 | 1.5 | 0.3 | 0.3 |
PDB ID | 8GD0 | 8GJT | 8GCZ | 8GD1 | 8GD3 | 8GD5 |
VSV-G Pseudovirus | HIV-1CH58TF | HIV-1JRFL | HIV-1AD8 | |
---|---|---|---|---|
DMSO | >100 | >100 | >100 | >100 |
BNM-III-170 | >100 | 0.033 ± 0.01 | 13.49 ± 6.65 | 3.75 ± 1.3 |
MCG-IV-210 | >100 | 3.46 ± 1.06 | >100 | >100 |
TFH-I-070-A6 | >100 | 0.45 ± 0.09 | 67.24 ± 30 | 9.59 ± 3.4 |
TFH-I-116-D1 | >100 | 0.065 ± 0.01 | 43.82 ± 16.6 | 4.8 ± 1.7 |
ZXC-I-090 | >100 | 2.63 ± 0.5 | >100 | >100 |
ZXC-I-092 | >100 | 0.75 ± 0.12 | 54.22 ± 22.8 | 34.05 ± 13.8 |
DL-I-101 | >100 | 0.16 ± 0.03 | >100 | 10.21 ± 3.1 |
DL-I-102 | >100 | 0.66 ± 0.25 | >100 | 87.02 ± 39 |
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Share and Cite
Ding, S.; Tolbert, W.D.; Zhu, H.; Lee, D.; Marchitto, L.; Higgins, T.; Zhao, X.; Nguyen, D.; Sherburn, R.; Richard, J.; et al. Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC. Viruses 2023, 15, 1185. https://doi.org/10.3390/v15051185
Ding S, Tolbert WD, Zhu H, Lee D, Marchitto L, Higgins T, Zhao X, Nguyen D, Sherburn R, Richard J, et al. Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC. Viruses. 2023; 15(5):1185. https://doi.org/10.3390/v15051185
Chicago/Turabian StyleDing, Shilei, William D. Tolbert, Huile Zhu, Daniel Lee, Lorie Marchitto, Tyler Higgins, Xuchen Zhao, Dung Nguyen, Rebekah Sherburn, Jonathan Richard, and et al. 2023. "Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC" Viruses 15, no. 5: 1185. https://doi.org/10.3390/v15051185
APA StyleDing, S., Tolbert, W. D., Zhu, H., Lee, D., Marchitto, L., Higgins, T., Zhao, X., Nguyen, D., Sherburn, R., Richard, J., Gendron-Lepage, G., Medjahed, H., Mohammadi, M., Abrams, C., Pazgier, M., Smith, A. B., III, & Finzi, A. (2023). Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC. Viruses, 15(5), 1185. https://doi.org/10.3390/v15051185