Question

how to increase a binding between a ligand ( etravirine) and a protein ( Human immunodeficiency virus type 1 HIV-1). disscusion should be based on thermodynamic theory

Answer 1

Ligands that bind to the allosteric site impair enzyme action by a wedge mechanism; they hinder domain mobility, opening and closing access to the active site. Final allosteric site architecture is achieved upon binding of the ligand. This flexibility and the possible clash between protein and ligand was accounted for by using a large overlap volume (100 Å3). Lack of systematic differences between binding to the wt versus the mutated enzyme indicates that activity against mutants is connected with the structural features of the ligand, rather than the energy of their binding. Interactions within the allosteric site are mostly associated with van der Waals forces and, to a lesser extent, hydrogen bonding. Ligand H18 exhibited the strongest binding to all forms of the enzyme, however, as mentioned above, it is a DJZ ligand that shows the largest change in binding energy when moving from the wt to the mutated enzymes. Its success seems to come from hydrogen bonding to lysine 101 rather than frequently mutated lysine 103. Furthermore, its orientation within the pocket is improved by a stronger and stiffer hydrogen bond from piperidine to histidine.

In docking, 107 structures of HIV-1 reverse transcriptase with ligands bound in the allosteric site (available from the Protein Data Bank) were used. This included 72 structures of the wild type enzyme: 1bqm, 1c0t, 1dtq, 1dtt, 1fk9, 1hpu, 1hpz, 1ikw, 1rt2, 1rt4, 1s6p, 1s9e, 1suq, 1sv5, 1tkt, 1tkx, 1tkz, 1tl1, 1tl3, 1vrt, 1vru, 2be2, 2hnd, 2jle, 2opp, 2rf2, 2rki, 2vg5, 2vg6, 2vg7, 2wom, 2won, 2ykm, 2ykn, 2yng, 2ynh, 2yni, 2zd1, 3dle ,3dlg, 3drp, 3hvt, 3irx, 3is9, 3lak, 3lal, 3lam, 3lan, 3lp0, 3lp1, 3m8p, 3m8q, 3mec, 3mee, 3qip, 3qlh, 3qo9, 3v81, 3v81, 4b3q, 4g1q, 4i2p, 4i2q, 4i7f, 4icl, 4ko0, 4puo, 4pwd, 4q0b, 5cym, 5cyq, and 5k14, out of which three structures (4puo, 4pwd, and 4q0b) were tetramers with slightly different allosteric site architecture. For these three structures, binding of ligands to both sites was studied. Furthermore, 32 structures of the mutated RT enzyme: 1bqn, 1fko, 1fkp, 1ikv, 1jkh, 1jla, 1jlc, 1jlg, 1lw0, 1lwc, 1lwe, 1lwf, 1s1t, 1s1u, 1s1v, 1s1w, 1s1x, 2hny, 2ic3. 2opq. 2opr, 2ops, 2ynf, 2ze2, 3bgr, 3dm2, 3dmj, 3dok, 3dol, 3med, 3meg, and 5fdl were studied, bearing 12 types of mutations, with the most dominant mutation being K103N followed by Y181C. The set included six double mutations and one triple mutation. In the considered structures, 48 ligands were present. They represented a number of different classes of chemicals. By far the most frequently studied (25 entries) ligand was NVP. Codes and structures of the remaining ligands are presented in Table 5. We have excluded the AC7 ligand from the QSAR studies because its polarized surface area by far exceeded that of the other ligands. This could have potentially led to erroneous results as the allosteric cavity is hydrophobic and the QO9 ligand, for example, contains silicon atoms, for which there is no parametrization.