Table 7 Relative binding energies (BE), inhibition constants, and interactions of GyrA WT and MTs with control antibiotics and best 3 lead compounds.
From: Exploring the potential role of GyrA inhibiting quinoline analog: an in silico study
Ligands | Target proteins (WT & MTs) | Binding energy (kcal/mol) | Inhibition constant (µM) | Conventional H-bond | Van der Waals interactions |
|---|---|---|---|---|---|
CIP | gyrA | – 7.32 | 4.35 | Lys42, Arg91, Asn165 | His45, Thr88, Leu102, Leu166, Val168, Asn169, Ser171 |
gyrA_T83I | – 6.92 | 8.43 | Lys42, Arg91, Asn165 | His45, Thr88, Ser97, Leu102, Leu166, Val168, Ser171, Tyr267 | |
gyrA_D87G | – 7.11 | 6.14 | Lys42, Arg91, Asn165 | Gly40, Leu41, His45, Thr88, Leu98, Leu102, Leu166,Val168, Asn169, Ser171, ser172, Tyr267 | |
gyrA_D87N | – 7.26 | 4.73 | Lys42, Arg91, Asn165 | His45, Thr88, Leu102, Leu166,Val168, Asn169, Ser171, Ser172 | |
gyrA_D87Y | – 7.09 | 6.34 | Lys42, Arg91, Asn165 | Gly40, Leu41, His45, Thr88, Leu102, Leu166,Val168, Asn169, Ser171, Ser172, Tyr267 | |
gyrA_T83I_D87N | – 7.06 | 6.67 | Lys42, Arg91, Asn165 | Gly40, Leu41, His45, Thr88, Leu102, Leu166,Val168, Asn169, Ser171, Ser172 | |
Average BE & Inh. const. of CIP | – 7.13 | 6.11 | |||
LEV | gyrA | – 6.66 | 13.13 | Arg91, Asn169, Ser172 | Gly40, Leu41, Thr88, Leu134, Asn165, Ser171 |
gyrA_T83I | – 6.59 | 14.76 | Arg91, Asn169, Ser172 | Gly40, Leu41, Thr88, Leu134, Asn165, Ser171 | |
gyrA_D87G | – 6.65 | 13.32 | Arg91, Asn169, Ser172 | Gly40, Leu41, Thr88, Leu134, Asn165, Ser171 | |
gyrA_D87N | – 6.42 | 19.8 | Arg91, Asn169, Ser172 | Gly40, Leu41, His45, Thr88, Leu134, Asn165, Ser171 | |
gyrA_D87Y | – 6.67 | 12.96 | Arg91, Asn169, Ser172 | Gly40, Leu41, Thr88, Leu134, Asn165, Ser171 | |
gyrA_T83I_D87N | – 6.47 | 18.08 | Lys42, Thr88, Arg91 | Gly40, Val44, His45, Asn87, Leu98, Leu102, Leu166, Asn169, Ser171, Ser172 | |
Average BE & Inh. const. of LEV | – 6.58 | 15.34 | |||
M2 | gyrA | – 8.13 | 1.1 | Lys42, Gly170, Ser172 | Pro35, Gly40, His45, Thr88, Arg91, Leu98, Leu102, Asn165, Leu166, Asn169 |
gyrA_T83I | – 8.1 | 1.16 | Lys42, Gly170, Ser172 | Pro35, Gly40, His45, Thr88, Arg91, Leu98, Leu102, Asn165, Leu166, Asn169 | |
gyrA_D87G | – 8.15 | 1.06 | Lys42, Gly170, Ser172 | Pro35, Gly40, His45, Thr88, Arg91, Leu98, Leu102, Asn165, Leu166, Asn169 | |
gyrA_D87N | – 8.14 | 1.09 | Lys42, Gly170, Ser172 | Pro35, Gly40, His45, Thr88, Arg91, Leu98, Leu102, Asn165, Leu166, Asn169 | |
gyrA_D87Y | – 8.12 | 1.12 | Lys42, Gly170, Ser172 | Pro35, Gly40, His45, Thr88, Arg91, Leu98, Leu102, Asn165, Leu166, Asn169 | |
gyrA_T83I_D87N | – 8.17 | 1.03 | Lys42, Gly170, Ser172 | Pro35, Gly40, His45, Thr88, Arg91, Leu98, Leu102, Asn165, Leu166, Asn169 | |
Average BE & Inh. const. of M2 | – 8.14 | 1.09 | |||
M9 | gyrA | – 7.3 | 4.44 | Lys42 | Gly40, His45, Arg91, Met92, Asn165, Leu166, Asn169, Gly170, Ser171 |
gyrA_T83I | – 7.29 | 4.51 | Lys42 | Gly40, His45, Arg91, Leu102, Asn165, Leu166, Asn169, Gly170, Ser171 | |
gyrA_D87G | – 7.38 | 3.92 | Lys42 | Pro35, Gly40, His45, Arg91, Met92, Leu102, Asn165, Leu166, Asn169, Gly170, Ser171 | |
gyrA_D87N | – 7.31 | 4.41 | Lys42 | Gly40, His45, Arg91, Met92, Leu102, Asn165, Leu166, Asn169, Gly170, Ser171 | |
gyrA_D87Y | – 7.34 | 4.15 | Lys42 | Pro35, Gly40, His45, Arg91, Met92, Leu102, Asn165, Asn169, Gly170, Ser171 | |
gyrA_T83I_D87N | – 7.46 | 3.41 | Lys42 | Pro35, Gly40, His45, Arg91, Met92, Leu102, Asn165, Leu166, Asn169, Gly170, Ser171 | |
Average BE & Inh. const. of M9 | – 7.35 | 4.14 | |||
M11 | gyrA | – 7.33 | 4.26 | Lys42, Ser172 | Gly40, Leu41, His45, Arg91, Met92, Asn169, Gly170, Ser171 |
gyrA_T83I | – 7.41 | 3.13 | His 45 | Pro35, Val44, Leu102, Asn165, Leu166, Asn169, Gly170, Ser171 | |
gyrA_D87G | – 7.64 | 2.54 | Lys42, His45 | Pro35, Gly40, Val44, Thr88, Leu102, Asn165, Leu166, Asn169, Gly170, Ser171 | |
gyrA_D87N | – 7.59 | 2.68 | Lys42,His45 | Pro35, Gly40, Val44, Thr88, Leu102, Asn165, Leu166, Asn169, Gly170, Ser171 | |
gyrA_D87Y | – 7.22 | 5.03 | Lys42, Ser172 | Gly40, Leu41, His45, Arg91, Met92, Gly170, Ser171 | |
gyrA_T83I_D87N | – 7.32 | 4.32 | Lys42 | Gly40, His45, Arg91, Leu98, Leu102, Asn169, Ser171 | |
Average BE & Inh. const. of M11 | – 7.42 | 3.6 | |||
