Targeting Caspase 8: Using Structural and Ligand-Based Approaches to Identify Potential Leads for the Treatment of Multi-Neurodegenerative Diseases
Abstract
:1. Introduction
2. Results and Discussion
2.1. Pharmacophore Modeling: 3D Pharmacophore Generation
2.2. Pharmacophore-Based Virtual Screening (PBVS)
2.3. Molecular Dynamics Simulation and Molecular Docking
2.4. Thermodynamics Analysis
2.5. Physical Properties of Ligands
3. Materials and Methods
3.1. Common Feature Pharmacophore Model
3.2. Common Feature Pharmacophore Generation
3.3. Pharmacophore-Based Virtual Screening (PBVS)
3.4. Molecular Docking Studies
3.5. Molecular Dynamics Simulation
3.6. Thermodynamic Analysis
4. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Sample Availability: Not available. |
9 | Features | Rank | Direct Hit | Partial Hit | Max Fit |
---|---|---|---|---|---|
01 | RDHHHHH | 152.441 | 111111 | 000000 | 7 |
02 | RZHHHHH | 152.286 | 111111 | 000000 | 7 |
03 | RZHHHHH | 152.086 | 111111 | 000000 | 7 |
04 | RZHHHHH | 152.058 | 111111 | 000000 | 7 |
05 | RZHHHHH | 151.770 | 111111 | 000000 | 7 |
06 | RZHHHHH | 151.719 | 111111 | 000000 | 7 |
07 | RZHHHHH | 151.511 | 111111 | 000000 | 7 |
08 | RZHHHHH | 151.147 | 111111 | 000000 | 7 |
09 | RZHHHHH | 151.017 | 111111 | 000000 | 7 |
10 | RZHHHHH | 150.863 | 111111 | 000000 | 7 |
Ligand | MolDock Score | Rerank Score | Docking Score | Similarity | Fit Value |
---|---|---|---|---|---|
ZINC00959167 | −79.5965 | −68.8523 | −328.308 | −247.343 | 4.999 |
ZINC01234548 | −109.655 | −94.2736 | −362.447 | −248.796 | 4.79982 |
ZINC09212678 | −80.7085 | −69.2156 | −328.066 | −246.039 | 4.89982 |
ZINC01301026 | −72.0231 | −58.011 | −342.572 | −265.101 | 4.99982 |
ZINC03830398 | −76.8326 | −60.6093 | −345.951 | −270.038 | 4.922 |
ZINC06143162 | −88.6888 | −65.8386 | −339.951 | −250.383 | 4.4982 |
ZINC14671560 | −97.5435 | −77.8008 | −377.247 | −280.961 | 4.482 |
ZINC04534268 | −116.417 | −94.1023 | −440.055 | −309.038 | 4.9482 |
ZINC19370490 | −138.402 | −117.46 | −480.995 | −329.518 | 4.682 |
ZINC02775438 | −91.4008 | −67.6985 | −406.978 | −311.933 | 4.621 |
Time Period | Gold Fitness Score | Residues | |
---|---|---|---|
Hydrogen Bond | Hydrophobic Interaction | ||
0 ns | 53.78 | R179, Q283, Y290, S339, R341, N381 | R179, C285, S339, Y340, R341 |
5 ns | 53.30 | R179, K292, R341 | R179, Y290, K292, Y340, R341, P343 |
10 ns | 54.06 | R341 | R179, N180, Y290, V338, Y340, R341 |
15 ns | 58.12 | R179, R341, N342, G346, N381E | C285, T333, V338, S339, Y340, R341, E345, G346, T347, W348, N381E, Q385 |
20 ns | 51.50 | R179 | H237, C285, V338, Y340 |
Time Period | Gold Fitness Score | Residues | |
---|---|---|---|
Hydrogen Bond | Hydrophobic Interaction | ||
0 ns | 60.48 | R179, S236, C285, R341 | H237, C285, S339, Y340, R341, D381B, K381D, |
5 ns | 52.37 | R179 | R179, H237, C285, V338, R341, P343, N381E, |
10 ns | 55.96 | S339, R341 | R179, H237, C285, Y290, K292, S339, Y340, R341 |
15 ns | 57.52 | A332, R341, G383 | R179, N180, G181, D185, Q283, Y340, R341, G346, T347, D381A, N381E, G383, Q385, |
20 ns | 58.68 | R179, H237 | S175J, H237, C285, G287, D288, Y290, V338, Y340, R341, P343, |
Ligand | Electrostatic | Polar Solvation | Van der Waal | SASA | SAV | Binding Free Energy (KJ/mol) |
---|---|---|---|---|---|---|
Z-IETD-FMK | −81.44 (33.4) | −4.98 (4.5) | −121.622 (15.2) | −14.52 (1.25) | −159.2 (9.5) | −382.524 (29.45) |
Z-IETD-FMK | −155.45 (30.5) | 58.326 (10.5) | −140.4 (8.45) | −17.90 (2.58) | −198.5 (6.47) | −453.924 (45.98) |
Z-LEHD-FMK | −58.45 (21.25) | 212.670 (12.36) | −108.45 (19.585) | −19.07 (2.04) | −169.7 (7.8) | −143.08 (29.704) |
NP-DEVD_AOMK | −53.11 (48.90) | 80.37 (4.80) | −109. 48 (5.08) | −13.09 (1.08) | −117.9 (6.24) | −106.99 (34.19) |
NP-LETD-AOMK | −145.48 (46.2) | 254.051 (15.66) | −314. 94 (18.56) | −17.6 (1.69) | −178.56 (9.4) | −401.93 (26.78) |
NP-LEHD AOMK | −58.67 (45.09) | 198.07 (12.360) | −265.98 (14.8) | −11.04 (2.05) | −164.5 (2.63) | −302.12 (41.29) |
ZINC19370490 | −154.45 (4.22) | 109.45 (29.07) | −190.07 (26.6) | −19.05 (2.44) | −180.56 (4.5) | −434.68 (39.45) |
ZINC04534268 | −225.64 (79.82) | 76.697 (9.14) | −217.56 (78.2) | −17.89 (1.99) | −88.67 (2.6) | −484.063 (31.08) |
Properties | ZINC04534268 | ZINC19370490 |
---|---|---|
GI absorption | Low | Low |
BBB permeant | No | No |
P-gp substrate | No | Yes |
CYP1A2 inhibitor | No | No |
CYP2C19 inhibitor | No | No |
CYP2C9 inhibitor | No | No |
CYP2D6 inhibitor | No | No |
CYP3A4 inhibitor | No | No |
LogKp(skin permeation) | −6.67 cm/s | −14.17 cm/s |
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Ahmad, K.; Balaramnavar, V.M.; Chaturvedi, N.; Khan, S.; Haque, S.; Lee, Y.-H.; Choi, I. Targeting Caspase 8: Using Structural and Ligand-Based Approaches to Identify Potential Leads for the Treatment of Multi-Neurodegenerative Diseases. Molecules 2019, 24, 1827. https://doi.org/10.3390/molecules24091827
Ahmad K, Balaramnavar VM, Chaturvedi N, Khan S, Haque S, Lee Y-H, Choi I. Targeting Caspase 8: Using Structural and Ligand-Based Approaches to Identify Potential Leads for the Treatment of Multi-Neurodegenerative Diseases. Molecules. 2019; 24(9):1827. https://doi.org/10.3390/molecules24091827
Chicago/Turabian StyleAhmad, Khurshid, Vishal M. Balaramnavar, Navaneet Chaturvedi, Saif Khan, Shafiul Haque, Yong-Ho Lee, and Inho Choi. 2019. "Targeting Caspase 8: Using Structural and Ligand-Based Approaches to Identify Potential Leads for the Treatment of Multi-Neurodegenerative Diseases" Molecules 24, no. 9: 1827. https://doi.org/10.3390/molecules24091827
APA StyleAhmad, K., Balaramnavar, V. M., Chaturvedi, N., Khan, S., Haque, S., Lee, Y. -H., & Choi, I. (2019). Targeting Caspase 8: Using Structural and Ligand-Based Approaches to Identify Potential Leads for the Treatment of Multi-Neurodegenerative Diseases. Molecules, 24(9), 1827. https://doi.org/10.3390/molecules24091827