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Binding of Anti-Fusion Peptides with HIVgp-41
B. Strockbine, S. Mukherjee, N. Carrascal, R.C. Rizzo
Infection of a target cell by a virus requires fusion of the viral
envelope and the target cell plasma membrane. Fusion events during infection
by human immunodeficiency virus (HIV) are mediated by a viral glycoprotein
called HIVgp41. Prior experimental studies of the core domain of HIVgp41
have revealed a structure containing a trimer-of-hairpin motif in which
three outer C-helices loop and wrap around three inner N-helices [1]. During
fusion, a proposed intermediate state transiently exposes both inner and
outer helices. Inhibitors designed to bind to the inner N-helices can
prevent reformation of the fusogenic structure thereby inhibiting virus-host
cell membrane fusion [2,3]. In 2003 the FDA approved the first inhibitor in
this anti-fusion class, Fuzeon (T20), a 36 amino acid C-helix peptide mimic
which specifically targets gp41 [4].
In this work we use computational methods to model binding of
“second generation” anti-fusion peptides complexed with HIVgp41 and use the
accompanying energetic and structural results to estimate binding affinities
for comparison with reported experimental activities [5]. These peptides are
of a different sequence than T20 and contain functionality which overlaps
with a highly conserved hydrophobic pocket described by Kim and coworkers
[1]. The pocket could be exploited both in the design of improved
anti-fusion peptides and for development of low molecular weight inhibitors.
Figure 1 shows how two Trp residues and one Ile on second generation
C-peptides pack into the interface formed by the inner N-helices [6,7].
These conserved pocket interactions are thought to play important roles in
stabilizing the fusogenic conformation of HIVgp41. The ability to delineate
which interactions are most important will ultimately enable the design of
better inhibitors with improved ability to combat resistance mutations.
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| Figure 1. A surface model of the inner helices
of HIVgp41 showing the hydrophobic pocket with the partnering
residues from the C-helix shown as ball and stick models. |
Figure 2. HIVgp41 inner N-helices represented in blue all
atom models with the C34 C-helix peptide represented in red ball and
stick with the parent Trp residue in the hydrophobic shown in green. |
Chan et al. [6] have shown that the ability to inhibit fusion directly
correlates with melting temperatures (Tm) for complexes containing
C-peptides that interact directly with the hydrophobic pocket. Experiments
with a peptide termed C34 (Figure 2 red peptide) revealed that changing the
parent Trp (green residue Figure 1) at position 631 to successively smaller
residues reduced the ability of the analogs to inhibit both viral entry and
cell membrane fusion [6]. A strong linear correlation between Tm of
complexes and the log of IC50 values was observed, which provides compelling
evidence that the experimental activities are a measure of peptide affinity
for the receptor, and that binding of C34 peptides containing the pocket
region is responsible for the observed inhibition [6]. In this work we use
all-atom molecular dynamics (MD) simulations followed by MM-GBSA (Molecular
Mechanics Generalized Born Surface Area) energy analyses to probe
structure-activity relationships (SAR) for a series of six C-peptides and
test current hypotheses about the importance of pocket residues for
modulating binding. A well tested computational model for this system will
assist the development of improved second generation anti-fusion peptides,
and will be useful for in silico high-throughput screening (docking)
of potential small molecule inhibitors.
Docking will be used to predict how compounds interact with the gp41 pocket
by considering thousands of different conformations, orientations, and the
electrostatic and steric complementarity of each protein-ligand complex. As
contributors to the DOCK program [8], we have recently optimized procedures
[9] for computing important desolvation terms associated with molecular
recognition. Specifically, we have added new algorithms to DOCK, based on
MM-GBSA methods, to more accurately estimate free energies of binding
[10,11]. Experimental testing for compounds suggested to bind tightly to
gp41 will be done in collaboration with Dr. Miriam Gochin at the University
of California at San Francisco (San Francisco, California). Compounds
suggested by computational docking and determined experimentally to bind
will be analyzed with in vitro syncytium and HIV viral infectivity assays.
The long-term goal of Dr. Rizzo's research is to develop promising
non-peptide drug candidates for HIV-1 fusion inhibition. We gratefully
acknowledge support from the Department of Applied Mathematics at Stony
Brook, the NYSTAR James D. Watson Investigator Program, and the
Computational Science Center at Brookhaven National Laboratory.
References
- [1] Chan, D.C., Fass, D., Berger, J.M., and Kim, P.S. Core structure
of gp41 from the HIV envelope glycoprotein. Cell 89 (2): 263-273 (1997).
- [2] Eckert, D.M. and Kim, P.S. Mechanisms of viral membrane fusion
and its inhibition. Annu. Rev. Biochem 70: 777-810 (2001).
- [3] Jiang, S., Lin, K., Strick, N., and Neurath, A.R. HIV-1
inhibition by a peptide. Nature 365: 113 (1993).
- [4] Poveda, E., Briz, V., and Soriano, V. Enfuvirtide, the first
fusion inhibitor to treat HIV infection. Aids Reviews 7 (3): 139-147
(2005).
- [5] Strockbine, B. and Rizzo, R.C. Binding of anti-fusion peptides
with HIVgp41 from molecular dynamics simulations: Quantitative
correlation with experiment. Proteins: Struct., Funct., Bioinf.
Submitted, 2006.
- [6] Chan, D.C., Chutkowski, C.T., and Kim, P.S. Evidence that a
prominent cavity in the coiled coil of HIV type 1 gp41 is an attractive
drug target. Proc. Natl. Acad. Sci. U.S.A. 95 (26): 15613-15617 (1998).
- [7] Jiang, S. and Debnath, A.K. A salt bridge between an N-terminal
coiled coil of gp41 and an antiviral agent targeted to the gp41 core is
important for anti-HIV-1 activity. Biochem. Biophys. Res. Commun. 270
(1): 153-157 (2000).
- [8] Jiang, S. and Debnath, A.K. A salt bridge between an N-terminal
coiled coil of gp41 and an antiviral agent targeted to the gp41 core is
important for anti-HIV-1 activity. Biochem. Biophys. Res. Commun. 270
(1): 153-157 (2000).
- [9] Rizzo, R.C., Aynechi, T., Case, D.A., and Kuntz, I.D. Estimation
of absolute free energies of hydration using continuum methods: Accuracy
of partial charge models and optimization of nonpolar contributions. J.
Chem. Theory Comp. In press, 2005.
- [10] Srinivasan, J., Cheatham, T.E., Cieplak, P., Kollman, P.A., and
Case, D. A. Continuum solvent studies of the stability of DNA, RNA, and
phosphoramidate - DNA helices. J. Amer. Chem. Soc. 120 (37): 9401-9409
(1998).
- [11] Srinivasan, J., Cheatham, T.E., Cieplak, P., Kollman, P.A., and
Case, D. A. Continuum solvent studies of the stability of DNA, RNA, and
phosphoramidate - DNA helices. J. Amer. Chem. Soc. 120 (37): 9401-9409
(1998).
Last Modified: January 31, 2008
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