Introduction: HIV viral envelope proteins are targets for small inhibitor
molecules aimed at disrupting the cellular entry process. Potential peptide-class inhibitor
molecules (rDNA drugs) have been previously identified, with mixed results,
through biomimicry and phage display experimental methods. Here we describe a
new approach based on computational fragment discovery. The method has the potential
to not only optimize peptide binding affinity but also to rapidly produce alternative
inhibitors against mutated strains.
Methods: A comprehensive, all-atom implicit solvent method is used to bombard
the C-heptad repeat unit of HIV-1 target envelope protein GP41 with single Damino
acid residues as they exist in their native state. A nascent peptide computational
search process then identifies potential favorable sequences of attached ligands based on four
peptide bond criteria. Finally, dynamic simulations of nascent peptides attached to host targets help refine
potential peptide inhibitors for experimental HIV-1 challenge assays and testing.
Results and Discussion: Initial testing of the method was done using 64,000 total ligands of D-amino
acid residues at a total computational time of 0.05 microseconds per ligand, which resulted in several
thousand attached ligands. Peptide bond criteria search employing three of the four bond constraints
with a tolerance of 20 percent, resulted in four potential peptide inhibitors of 5 to 6 residues in length.
Only one of the four peptides demonstrated IC50 values and partial viral inhibition based on cell challenge
assays using CEM-SS host cells. That peptide inhibitor also computationally demonstrated longtime
attachment and stability to a helical groove in its C-heptad target. This initial testing of peptide
fragment discovery against HIV-1 has helped us refine the protocols and identify key areas of improvement.
Conclusion: Our methods demonstrate the potential to design efficient peptide inhibitors to viral target
proteins based on an all-atom dynamic simulation and using a ligand library as fragments of potential
nascent peptides. Our methods can be greatly improved through the use of higher numbers of ligands,
increased time of bombardment, and tighter constraints on the peptide bond search step. Our method
may be important in the need to rapidly respond to target mutations and to advance multiple targeting
methods based multiple peptide inhibitors.