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. Arp2/3 complex is an assembly of seven proteins which regulates actin dynamics by promoting the nuclation of actin filament branches from pre-existing filaments. Branched actin networks created by Arp2/3 complex function play a central role in many cellular processes, including cell motility, podosome formation and invasion of host cells by pathogens. We previously reported the crystal structures of two classes of small molecule inhibitors which inhibit Arp2/3 complex in vito and in vivo. These compounds inhibit the complex with IC50 values in the low micromolar range. Here we propose to use free energy perturbation calculations to computationally explore the effect of small chemical alterations on the compounds on their energy of binding to the complex. Our ultimate goal is to derive inhibitors with low nanomolar affinity from the original compounds. Such inhibitors will be invaluable for cell biologists studying Arp2/3 complex function in vivo and may be useful in inhibiting migration of tumor cells during metastasis.
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