(15g) Understanding the Antagonistic Mechanism of a De Novo Designed Peptide With Experimental HIV Fusion Inhibition Via Molecular Simulation

A noble goal in protein design is to predict the potency and understand in detail the mechanism of inhibition of a candidate antagonist. Previous de novo design has produced several HIV fusion inhibitors targeting HIV-gp41¹. These inhibitors were experimentally confirmed to inhibit viral entry.  Here, we probe, through computational studies based on molecular dynamics simulations the mechanism of inhibition of SQ175, a design among the best in antagonistic activity.

Multiple independent explicit solvent (TIP3) molecular dynamics simulations of SQ175 bound to the trimeric coiled-coil are performed in the AMBER² MD package. Using the snapshots from the trajectories, interaction maps were constructed identifying key SQ175:gp41 hydrophobic and electrostatic interactions. Binding free energy calculations of SQ175 confirm its affinity for the trimeric coiled-coil of gp41. Subsequently, in CHARMM³ and using generalized Born implicit solvent⁴, simulations of the C-terminus binding fragment bound to the trimeric coiled-coil of gp41 were performed. These simulations aimed at evaluating the native interactions between the C-terminus binding fragment:trimeric core and to construct a map denoting the minimum Cα-Cα distances the C-terminus binding fragment residues experience with respect to the gp41 trimeric coiled-coil. Next, multiple independent docking simulations of the C-terminus binding fragment starting 10-12 Å away from its fusion intermediate structure were performed, where after the MD, the C-terminus binding fragment was found to spontaneously dock within 1.5 Å of its conformation in the crystal structure in one simulation, indicating the system behaves well. Then, in the presence of SQ175, 12 independent docking simulations were performed starting from 12 different initial coordinates to mimic the C-terminus binding fragment approaching gp41. No restraints were implemented to drive them together. The SQ175 peptide was observed to dramatically reduce the number of native C-terminus binding fragment:gp41 contacts of which several are necessary for HIV fusion and subsequent entry, as observed by minimum Cα-Cα distances. The antagonist SQ175 was observed to stably bind to the trimeric coiled-coil of gp41 and physically block a large fraction of the native C-terminus binding fragment:gp41 contacts. Based on these results, new insights for future generations of fusion inhibitors are described.

References

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