A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa
Abstract
:1. Introduction
2. Results and Discussion
2.1. Protein Structural Alignment
2.2. Protein Sequence Alignment
2.3. Molecular Docking
2.3.1. Score in Place
2.3.2. Cognate Docking
2.3.3. Cross Docking
2.4. Pharmacophore Modeling
3. Materials and Methods
3.1. Dataset
3.2. Protein Preparation
3.3. Protein Structural Alignment
3.4. Protein Sequence Alignment
3.5. Ligand Preparation
3.6. Molecular Docking
3.7. Pharmacophore Modeling
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Sample Availability
References
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PDB ID | H-Bond | Halogen Bond | Pi-Pi Stacking | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
5TNT | FIXa | Asp189 | Ser190 | Gly216 | Gly216 | Phe174 | - | - | ||||
5TNO | Asp189 | Ser190 | Gly216 | Gly216 | - | - | - | |||||
5EGM | - | - | Gly216 | Gly216 | - | - | His147 | |||||
4ZAE | - | - | Gly216 | Gly216 | Phe174 | - | - | |||||
4Z0K | - | - | Gly216 | - | Phe174 | Trp215 | - | |||||
4YZU | - | - | - | - | Phe174 | Trp215 | - | |||||
2W26 | FXa | - | Gly219 | - | - | Tyr99 | ||||||
2P16 | Gly216 | - | Glu146 | - | - | Tyr99 | ||||||
3KL6 | Gly216 | Gly219 | Gln192 | Glu97 | - | - | Tyr99 | |||||
2PHB | Gly216 | Gly219 | - | Phe174 | Trp215 | Tyr99 | ||||||
3M36 | Asp189 | Ala190 | Gly216 | - | Phe174 | Trp215 | Tyr99 | |||||
2XBX | - | - | Gly216 | Gly218 | - | Phe174 | Trp215 | Tyr99 |
FIXa | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid 5TNT | Grid 5TNO | Grid 5EGM | Grid 4ZAE | Grid 4Z0K | Grid 4YZU | |||||||
Gscore (kcal/mol) | Gscore (kcal/mol) | GScore (kcal/mol) | GScore (kcal/mol) | GScore (kcal/mol) | GScore (kcal/mol) | |||||||
1 | 5TNT | −9.95 | 5TNT | −9.65 | 5EGM | −9.85 | 2XBX | −9.86 | 4Z0K | −10.33 | 4YZU | −9.71 |
2 | 5TNT | −9.77 | 5TNO | −9.38 | 5EGM | −9.79 | 3KL6 | −9.56 | 4Z0K | −9.50 | 4YZU | −9.63 |
3 | 5TNT | −9.60 | 5TNT | −9.18 | 5EGM | −9.17 | 2XBX | −9.41 | 5TNT | −8.81 | 3KL6 | −9.49 |
4 | 2XBX | −8.29 | 5TNO | −8.89 | 4Z0K | −8.45 | 3M36 | −9.35 | 5TNO | −8.81 | 4ZAE | −9.29 |
5 | 3KL6 | −8.17 | 5TNO | −8.58 | 2XBX | −8.15 | 2XBX | −9.21 | 2XBX | −8.54 | 3KL6 | −9.23 |
6 | 2XBX | −8.06 | 4Z0K | −8.58 | 2XBX | −8.12 | 2XBX | −9.15 | 5TNO | −8.52 | 2XBX | −9.09 |
7 | 2XBX | −7.89 | 2XBX | −8.54 | 2XBX | −8.10 | 2XBX | −9.06 | 5TNO | −8.50 | 3KL6 | −9.03 |
8 | 2PHB | −7.81 | 4Z0K | −8.28 | 4Z0K | −8.04 | 2PHB | −8.97 | 4YZU | −8.36 | 3KL6 | −8.98 |
9 | 2PHB | −7.70 | 2W26 | −8.07 | 2XBX | −8.01 | 2XBX | −8.90 | 5TNO | −8.30 | 4YZU | −8.96 |
10 | 2XBX | −7.68 | 3KL6 | −7.95 | 2XBX | −7.88 | 3M36 | −8.89 | 5TNO | −8.20 | 4ZAE | −8.96 |
11 | 2XBX | −7.63 | 5TNT | −7.84 | 2XBX | −7.86 | 2XBX | −8.80 | 2XBX | −7.73 | 4YZU | −8.85 |
12 | 2XBX | −7.60 | 2PHB | −7.83 | 2W26 | −7.85 | 3KL6 | −8.72 | 4YZU | −7.73 | 3KL6 | −8.81 |
13 | 2PHB | −7.57 | 2PHB | −7.82 | 2PHB | −7.60 | 2PHB | −8.71 | 2XBX | −7.68 | 2XBX | -8.73 |
14 | 2PHB | −7.53 | 2XBX | −7.78 | 2PHB | -7.49 | 2XBX | −8.71 | 2XBX | −7.66 | 2PHB | −8.70 |
15 | 2XBX | −7.47 | 2PHB | −7.68 | 2PHB | −7.47 | 2XBX | −8.66 | 2XBX | −7.61 | 2XBX | −8.62 |
16 | 2XBX | −7.47 | 3KL6 | −7.68 | 2W26 | −7.45 | 3KL6 | −8.65 | 2XBX | −7.56 | 2XBX | −8.48 |
17 | 2XBX | −7.37 | 2PHB | −7.68 | 2PHB | −7.35 | 3M36 | −8.62 | 5TNO | −7.52 | 2XBX | −8.48 |
18 | 2PHB | −7.36 | 2XBX | −7.65 | 2W26 | −7.11 | 3M36 | −8.62 | 2W26 | −7.37 | 3KL6 | −8.47 |
19 | 2PHB | −7.35 | 2W26 | −7.62 | 2PHB | −7.05 | 5TNT | −8.61 | 2PHB | −7.35 | 2W26 | −8.45 |
20 | 3KL6 | −7.34 | 2XBX | −7.60 | 2PHB | −7.03 | 3KL6 | −8.57 | 2XBX | −7.32 | 3KL6 | −8.39 |
21 | 2XBX | −7.33 | 2PHB | −7.58 | 2PHB | −6.99 | 2XBX | −8.54 | 2XBX | −7.24 | 2XBX | −8.39 |
22 | 3KL6 | −7.30 | 2PHB | −7.54 | 2W26 | −6.98 | 2PHB | −8.49 | 2XBX | −7.19 | 3KL6 | −8.39 |
23 | 3KL6 | −7.21 | 2XBX | −7.46 | 2XBX | −6.98 | 2PHB | −8.46 | 3KL6 | −7.18 | 2W26 | −8.37 |
24 | 2PHB | −7.20 | 2PHB | −7.41 | 2W26 | −6.97 | 2P16 | −8.43 | 2W26 | −7.13 | 2W26 | −8.30 |
25 | 3KL6 | −7.13 | 3KL6 | −7.37 | 2PHB | −6.93 | 2PHB | −8.43 | 3KL6 | −7.13 | 2XBX | −8.29 |
26 | 2PHB | −7.07 | 3KL6 | −7.33 | 5TNT | −6.87 | 5TNT | −8.40 | 3KL6 | −7.06 | 3KL6 | −8.29 |
27 | 2XBX | −7.04 | 2XBX | −7.33 | 2PHB | −6.72 | 2PHB | −8.40 | 2PHB | −7.00 | 4ZAE | −8.19 |
28 | 2XBX | −7.04 | 2PHB | −7.31 | 2PHB | −6.63 | 2XBX | −8.40 | 2W26 | −6.99 | 2XBX | −8.16 |
29 | 2PHB | −6.85 | 2PHB | −7.31 | 2PHB | −6.59 | 3KL6 | −8.39 | 3KL6 | −6.97 | 2XBX | −8.00 |
30 | 3KL6 | −6.83 | 2XBX | −7.27 | 2W26 | −6.45 | 3KL6 | −8.31 | 2PHB | −6.95 | 2XBX | −7.93 |
FXa | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid 2W26 | Grid 2P16 | Grid 3KL6 | Grid 2PHB | Grid 3M36 | Grid 2BXB | |||||||
GScore (kcal/mol) | GScore (kcal/mol) | GScore (kcal/mol) | GScore (kcal/mol) | GScore (kcal/mol) | GScore (kcal/mol) | |||||||
1 | 3M36 | −11.46 | 2P16 | −11.48 | 2XBX | −12.95 | 2XBX | −11.90 | 3M36 | −13.78 | 2XBX | −14.83 |
2 | 2XBX | −11.00 | 2XBX | −11.07 | 2XBX | −12.61 | 2XBX | −11.87 | 3M36 | −13.73 | 2XBX | −14.81 |
3 | 2PHB | −10.91 | 2XBX | −11.03 | 2XBX | −12.56 | 3M36 | −11.85 | 3M36 | −12.41 | 2XBX | −14.58 |
4 | 2XBX | −10.89 | 2XBX | −11.02 | 2XBX | −12.55 | 3M36 | −11.69 | 3M36 | −12.34 | 2PHB | −14.26 |
5 | 3M36 | −10.85 | 2XBX | −11.01 | 3KL6 | −12.35 | 2XBX | −11.64 | 3M36 | −11.65 | 2PHB | −14.09 |
6 | 2XBX | −10.80 | 3M36 | −10.73 | 2PHB | −12.28 | 2XBX | −11.52 | 3M36 | −11.35 | 2PHB | −13.00 |
7 | 2PHB | −10.73 | 3M36 | −10.65 | 2XBX | −12.27 | 3M36 | −11.49 | 2P16 | −9.06 | 2PHB | −12.86 |
8 | 3M36 | −10.72 | 2P16 | −10.63 | 3KL6 | −12.14 | 2PHB | −11.18 | 2XBX | −9.00 | 3M36 | −12.68 |
9 | 2XBX | −10.47 | 2PHB | −10.47 | 2P16 | −12.11 | 2PHB | −11.08 | 2XBX | −8.75 | 2XBX | −11.65 |
10 | 2P16 | −10.34 | 2PHB | −10.42 | 2PHB | −11.96 | 2PHB | −11.07 | 2P16 | −8.65 | 2PHB | −11.63 |
11 | 2XBX | −10.33 | 2PHB | −10.40 | 2XBX | −11.90 | 2XBX | −10.82 | 2PHB | −8.62 | 2PHB | −11.54 |
12 | 2XBX | −10.26 | 2PHB | −10.38 | 3KL6 | −11.89 | 2XBX | −10.82 | 2PHB | −8.43 | 2XBX | −11.28 |
13 | 2PHB | −9.86 | 2PHB | −10.36 | 2XBX | −11.80 | 2XBX | −10.76 | 2P16 | −8.19 | 2PHB | −10.55 |
14 | 2PHB | −9.86 | 2XBX | −10.29 | 2P16 | −11.80 | 3M36 | −10.34 | 2XBX | −8.09 | 3M36 | −10.45 |
15 | 2W26 | −9.73 | 2XBX | −10.28 | 3KL6 | −11.79 | 2XBX | −10.22 | 2PHB | −7.94 | 2XBX | −9.72 |
16 | 3M36 | −9.70 | 3KL6 | −10.21 | 2P16 | −11.76 | 3M36 | −10.18 | 2PHB | −7.59 | 2PHB | −8.72 |
17 | 3M36 | −9.67 | 2XBX | −10.20 | 2PHB | −11.71 | 3M36 | −10.11 | 2PHB | −7.49 | 2PHB | −8.64 |
18 | 2PHB | −9.66 | 2XBX | −10.18 | 2PHB | −11.66 | 2PHB | −10.11 | 2PHB | −7.41 | 2PHB | −8.23 |
19 | 2PHB | −9.65 | 2PHB | −10.17 | 2PHB | −11.42 | 2XBX | −10.09 | 2PHB | −7.32 | 2XBX | −8.08 |
20 | 2PHB | −9.62 | 2XBX | −10.14 | 2PHB | −11.40 | 2P16 | −9.95 | 2PHB | −7.30 | 2XBX | −7.92 |
21 | 2P16 | −9.59 | 3M36 | −10.08 | 2PHB | −11.40 | 3KL6 | −9.83 | 2XBX | −7.24 | 2PHB | −7.23 |
22 | 3KL6 | −9.54 | 2PHB | −9.91 | 2PHB | −11.39 | 2XBX | −9.77 | 2PHB | −7.11 | 2PHB | −7.20 |
23 | 2XBX | −9.47 | 2P16 | −9.88 | 2PHB | −11.27 | 2XBX | −9.59 | 2PHB | −7.05 | 2XBX | −7.19 |
24 | 2PHB | −9.44 | 2PHB | −9.64 | 2PHB | −11.18 | 2XBX | −9.48 | 3KL6 | −6.98 | 2XBX | −5.35 |
25 | 2W26 | −9.40 | 2PHB | −9.63 | 2PHB | −11.13 | 3KL6 | −9.47 | 4ZAE | −6.86 | 4ZAE | −5.27 |
26 | 3KL6 | −9.37 | 3M36 | −9.58 | 3KL6 | −11.12 | 3KL6 | −9.39 | 2PHB | −6.74 | 4ZAE | −5.18 |
27 | 2W26 | −9.37 | 3KL6 | −9.46 | 2XBX | −11.01 | 2PHB | −9.28 | 2PHB | −6.70 | 4Z0K | −5.02 |
28 | 3KL6 | −9.36 | 3KL6 | −9.41 | 2XBX | −11.01 | 3KL6 | −9.28 | 3KL6 | −6.50 | 4ZAE | −4.98 |
29 | 3M36 | −9.36 | 2XBX | −9.40 | 3KL6 | −11.01 | 3KL6 | −9.21 | 4ZAE | −6.47 | 4Z0K | −4.94 |
30 | 2PHB | −9.35 | 2PHB | −9.38 | 2PHB | −11.00 | 2P16 | −9.11 | 2XBX | −6.44 | 4Z0K | −4.92 |
PDB ID | Resolution | Target | Ligand Name | hFIXa IC50 (nM) | hFXa IC50 (nM) | Score-In-Place | Cognate Docking | |
---|---|---|---|---|---|---|---|---|
GScore (kcal/mol) | GScore (kcal/mol) | RMSD (Å) | ||||||
5TNT | 1.40 Å | hFIXa | CFM-184 | 4.90 | 31000.00 | −9.78 | −9.95 | 0.31 |
5TNO | 1.54 Å | Selective ligand | 98.00 | >100000 | −10.14 | −9.38 | 0.90 | |
5EGM | 1.84 Å | Lead compound | 0.60 | 234.00 | −9.69 | −9.85 | 1.22 | |
4ZAE | 1.86 Å | Lead compound | 3.60 | 105.00 | −9.64 | not docked | - | |
4Z0K | 1.41 Å | Lead compound | 462.00 | - | −10.30 | −10.33 | 0.12 | |
4YZU | 1.41 Å | Inactive | 9000.00 | 62500.00 | −9.33 | −9.71 | 0.99 | |
2W26 | 2.08 Å | hFXa | Rivaroxaban | Selective | 0.70 | −9.65 | −9.73 | 0.20 |
2P16 | 2.30 Å | Apixaban | Selective | 0.08 | −11.52 | −11.48 | 0.46 | |
3KL6 | 1.45 Å | Letaxaban | Selective | 3.50 | −11.58 | −12.35 | 0.25 | |
2PHB | 2.30 Å | Eribaxaban | Selective | 0.32 | −11.18 | −11.18 | 1.37 | |
3M36 | 2.15 Å | DPC-423 | Selective | 0.15 | −13.71 | −13.78 | 0.00 | |
2XBX | 1.85 Å | Lead compound | - | 15.00 | −15.03 | −14.83 | 1.41 |
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Kundu, S.; Wu, S. A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa. Molecules 2021, 26, 5372. https://doi.org/10.3390/molecules26175372
Kundu S, Wu S. A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa. Molecules. 2021; 26(17):5372. https://doi.org/10.3390/molecules26175372
Chicago/Turabian StyleKundu, Sibsankar, and Sangwook Wu. 2021. "A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa" Molecules 26, no. 17: 5372. https://doi.org/10.3390/molecules26175372