RT Journal Article
SR Electronic
T1 Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.02.09.940510
DO 10.1101/2020.02.09.940510
A1 Cruz, Matthew A.
A1 Frederick, Thomas E.
A1 Singh, Sukrit
A1 Vithani, Neha
A1 Zimmerman, Maxwell I.
A1 Porter, Justin R.
A1 Moeder, Katelyn E.
A1 Amarasinghe, Gaya K.
A1 Bowman, Gregory R.
YR 2020
UL http://biorxiv.org/content/early/2020/02/10/2020.02.09.940510.abstract
AB Many proteins are classified as ‘undruggable,’ especially those that engage in protein-protein and protein-nucleic acid interactions. Discovering ‘cryptic’ pockets that are absent in available structures but open due to protein dynamics could provide new druggable sites. Here, we integrate atomically-detailed simulations and biophysical experiments to search for cryptic pockets in viral protein 35 (VP35) from the highly lethal Ebola virus. VP35 plays multiple essential roles in Ebola’s replication cycle, including binding the viral RNA genome to block a host’s innate immunity. However, VP35 has so far proved undruggable. Using adaptive sampling simulations and allosteric network detection algorithms, we uncover a cryptic pocket that is allosterically coupled to VP35’s key RNA-binding interface. Experimental tests corroborate the predicted pocket and confirm that stabilizing the open form allosterically disrupts RNA binding. These results demonstrate simulations’ power to characterize hidden conformations and dynamics, uncovering cryptic pockets and allostery that present new therapeutic opportunities.