Table 2 Docking scores, Glide energies, and H-bond interactions of the strongest binding trimers on PlGF and VEGF. All values are expressed as mean ± standard deviation based on the three strongest binding conformations
From: Systematic design and evaluation of aptamers for VEGF and PlGF biomarkers of Preeclampsia
Aptamer | Docking score (kcal/mol) | Glide Energy (kcal/mol) | H bond interactions | Cluster |
|---|---|---|---|---|
For PlGF | ||||
AGG | -6.734 ± 1.231 | -63.931 ± 7.338 | VAL51, HIS53, SER56, ASP71, GLU72, GLY94 | 1 |
GGG | -7.113 ± 0.876 | -66.900 ± 4.451 | VAL51, GLU52, PHE55, SER56, SER58, GLU72 | 1 |
CAA | -5.613 ± 1.944 | -57.960 ± 11.160 | ARG39, LEU40, ASP42, SER58, GLY67 | 3 |
GCG | -6.991 ± 1.020 | -66.597 ± 3.083 | TYR33, VAL51, GLU52, ASP71, GLU72 | 1 |
ACA | -6.889 ± 0.238 | -69.595 ± 1.999 | ARG38, SER58, GLY67, LEU74 | 3 |
GAG | -5.313 ± 0.920 | -65.236 ± 5.829 | ARG39, ASP42, GLY67, ASP71, GLU72 | 3 |
GCA | -5.050 ± 1.275 | -51.232 ± 4.580 | TYR33, PHR55, CYS69, GLY70, GLU72, CYS112 | 2 |
GCC | -4.976 ± 0.247 | -55.050 ± 3.267 | GLY30, TYE33, VAL108 | 2 |
For VEGF | ||||
AGG | -7.159 ± 0.214 | -56.639 ± 2.186 | GLU44, LYS84, HIS86, GLN87 | Not applicable |
AAA | -6.626 ± 1.094 | -56.234 ± 9.408 | GLU44, ARG82, LYS84, GLN87 | Not applicable |
CGG | -6.217 ± 0.907 | -51.246 ± 8.171 | GLU42, GLU44, ARG82, LYS84, GLN87 | Not applicable |
CGA | -6.883 ± 0.196 | -57.602 ± 2.794 | ASP41, GLU44, TYR45, LYS84, GLN87 | Not applicable |
GAA | -7.016 ± 0.025 | -59.915 ± 0.999 | GLU42, GLU44, LYS84, GLN87 | Not applicable |
CCG | -6.181 ± 0.747 | -47.148 ± 2.715 | GLU42, GLU44, LYS84, HIS86, GLN87 | Not applicable |
GGA | -6.261 ± 0.610 | -53.213 ± 3.850 | ASP41, GLU44, LYS84, GLN87 | Not applicable |
GAC | -6.373 ± 0.326 | -52.159 ± 2.615 | GLU42, GLU44, ARG82, LYS84, PRO85, GLN87 | Not applicable |
GGG | -6.572 ± 0.099 | -51.142 ± 0.420 | ASP41, GLU42, GLU44, LYS84, GLN87 | Not applicable |
CAC | -6.103 ± 0.455 | -54.774 ± 0.997 | LYS84, PRO85, GLN87 | Not applicable |