Structural insights into the binding of small ligand molecules to a G-quadruplex DNA located in the HIV-1 promoter.

Targeting guanine (G)-rich DNA sequences, folded into non-canonical G-quadruplex (G4) structures, by small ligand molecules is a promising strategy for gene therapy of various diseases. There is experimental proposal that, among eight studied ligands, nitidine chloride - NC and a benzo phenanthridine derivative - BPD have the highest binding affinity for such a sequence (5'-T1 G2 G3 C4 C5 T6 G7 G8 G9 C10 G11 G12 G13 A14 C15 T16 G17 G18 G19 -3') in the HIV-1 promoter, indicating that an anti-HIV-1 prodrug may regulate the expression of the promoter. Herein, this experimental indication is elaborated by using molecular docking simulations and by characterizing the modes of binding of the eight natural molecules to the particular G4. Moreover, the configurational entropy, as an upper bound of the true entropy contribution to the free energy in noncovalent binding, is employed to see into the structural changes experienced by the G4-DNA upon ligand binding. For various parts (complete structure, backbone, system of all bases, bases of G-tetrads) of the G4-DNA structure, a subtle molecular dynamics (MD) is exploited to determine the change of asymptotic (for infinitely long MD simulation) configurational entropy, being the thermodynamic consequence of DNA flexibility change upon complex formation. While NC increases rigidity of G4 (mainly through the system of all nucleobases), BPD increases flexibility of G4 (more than 50% stems from the sugar-phosphate backbone). These insights are further dissected and substantiated by considering the configurational entropy contributions at the level of individual base pairs making the two G-tetrads (G2 G7 G13 G17 and G3 G8 G12 G18 ) and by exploring the estimates of the total intra-base pair and inter-base pair entropies. This work makes the structural origin of enhanced stability of G4-DNA more certain - useful information when attempting to design optimal G4-DNA binders.