Exploration of the binding of benzimidazole-biphenyl derivatives to hemoglobin using docking and molecular dynamics simulation.
In this study, the binding of hemoglobin (Hb) with three benzimidazole-biphenyl derivatives (telmisartan (TST), candesartan (CST), and DB921) is investigated by molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation. Results demonstrate that the three drugs locate in the cavities formed by α1, α2, and β2 subunits. The average gyration radii are estimated and consistent with available experimental results. The binding free energies suggest that the binding site of CST/Hb is more stable than those of TST/Hb and DB921/Hb. The energy decomposition analysis is performed and reveals that the electrostatic interactions play an important role in the stabilization of the binding site of CST/Hb or DB921/Hb while the van der Waals interactions contribute largely to stabilization of the binding site of TST/Hb. The key residues stabilizing the binding sites of TST/Hb, CST/Hb, and DB921/Hb are identified based on the residue decomposition analysis. The probability densities of salt bridge distances demonstrate that there still exist the four salt bridges between α1 and α2 subunits of Hb in presence of these drugs.
Li
Jinyu
J
State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Xin MoFan Road No. 5, Nanjing 210009, China.
Shi
Rongwei
R
Yang
Cao
C
Zhu
Xiaolei
X
D000578:Amidines / Q000737:chemistry / Q000378:metabolism; D001562:Benzimidazoles / Q000737:chemistry / Q000378:metabolism*; D001565:Benzoates / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D001713:Biphenyl Compounds / Q000737:chemistry / Q000378:metabolism*; D006454:Hemoglobins / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D012492:Salts / Q000737:chemistry; D000077333:Telmisartan; D013777:Tetrazoles / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics; D013997:Time Factors
D000578:Amidines; D001562:Benzimidazoles; D001565:Benzoates; D001713:Biphenyl Compounds; D006454:Hemoglobins; D021122:Protein Subunits; D012492:Salts; D000077333:Telmisartan; D013777:Tetrazoles; C506617:DB 921; C010574:biphenyl; C081643:candesartan