Computational Evaluation of HIV‑1 gp120 Conformations of Soluble Trimeric gp140 Structures as Targets for de Novo Docking of First- and Second-Generation Small-Molecule CD4 Mimics

Small-molecule CD4
mimics (SMCM’s) bind to the gp120 subunit
of the HIV-1 envelope glycoprotein (Env) and have been optimized to
block cell infection in vitro. The lack of the V1/2 and V3 loops and
the presence of the β2/3 and β20/21 strands (bridging
sheet) in the available structures of the monomeric gp120 core may
limit its applicability as a target for further synthetic optimization
of SMCM potency and/or breadth. Here, we employ a combination of binding-site
search, docking, estimation of protein–ligand interaction energy,
all-atom molecular dynamics, and ELISA-based CD4-binding competition
assays to create, characterize, and rationalize models of first- and
second-generation of SMCM’s bound to the distinct, trimeric
BG505 SOSIP.664 structures 4NCO and 4TVP containing V1/2 and V3 loops with no bridging sheet. We demonstrate
that the in silico neutralization of the highly conserved D368 is
necessary to obtain the correct orientation of SMCM in their binding
site when docking against the monomeric gp120 core. The computational
results correlate with IC50’s measured in CD4 binding
competition ELISA and with KD’s
measured on gp120 core monomer. This supports the hypothesis that
the 4NCO trimeric
structure represents a viable target for further SMCM’s optimization
with advantages over both the 4TVP trimer and gp120 core monomer. Finally,
the docking protocol has been optimized to screen compounds that can
clearly interact with the highly conserved residue D368, increasing
the likelihood of future optimizations to arrive at SMCM’s
with a broader spectrum of activity.