MOLECULAR DYNAMICS STUDIES OF MUTANT HIV GP120 ENVELOP PROTEINS WITH BOUND HIV

Carnegie-Mellon University, Pittsburgh PA

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Judith LaLonde, Bryn Mawr College: Development of Novel HIV Entry Inhibitors Using the ROCS Shaped Based Matching Algorithm and Molecular Dynamics Studies of gp120 Envelop Proteins The key objective of this computational project is to rationally design small-molecule antagonists that block the interaction between the human CD4 cell-surface receptor and the gp120 envelop protein of HIV-1 as potential therapeutics for the treatment of AIDS. The viral envelop protein, gp120, undergoes a large conformational change upon binding to the cellular CD4 receptor allowing subsequent binding to the chemokine receptor and viral-host cell fusion (1). The NIH PO1 GM 56550 project team (Structure-Based Antagonism of HIV-1 Envelope Function in Cell Entry) has synthesized and assayed a series of NBD compound analogs (2) (Figure 1, B). These compounds compete with CD4 binding to gp120 and enhance binding of CD4:gp120 to the chemokine receptor CCR5. Elucidation of the thermodynamic properties of NBD compounds via ITC by Schon et al (2) indicates that this compound class induces the structuring of gp120 in a manor similar to CD4 binding. These compounds enhance inactive the virus prior to binding to the cellular receptor. A predicted binding mode for this class of compounds has been produced from computational docking studies using Glide (3, 4). Mutational analysis of the series of NBD compounds with key binding site residues has shown certain compounds and mutations increase binding affinity and enhance viral infectivity (10). This mutational data provides information of key protein interactions responsible for the agonistic properties of the compounds. Over the course of the current allocation I have constructed a conformer data base of the Zinc collection (11) of 8 million drug-like compounds and used the ROCS (12-14) shaped based virtual screening methods to develop new active analogues HIV gp120-CD4 binding. Molecular dynamics as implemented in AMBER (5) has been used to explore the dynamic fluctuations of the inhibitor NBD556 bound to wild type and various mutations of the gp120 envelope. Molecular dynamics 100 pico-second trajectories have been completed with over 64 gp120 envelop proteins complexed with various small molecules. A qualitative view of protein-ligand interactions during the simulation indicates an asymmetrical interaction of the tetramethyl substitutions on the piperadine ring. The trajectories of the wild-type and mutant proteins-ligand complexes are also being used to predict binding affinity using the MM/PBSA methodology (9) as implemented in Amber. Both ROCS based virtual screening and MD simulations will be continued during the next allocation period (4-1-10 to 3-31-11) A resource of 110,000 SU split between Warhol and Salk at the Pittsburgh Super Computing Center as well as Advanced Technical Support for implementation of PVM and optimization of algorithms when updates are available. Continued, rapid turn-over using the PSC resources will further enhance the structure-based discovery of HIV entry inhibitors.