
IBM's Summit simulates molecular dynamics to find Covid-19 therapeutics - turkeytotal
https://chemrxiv.org/articles/Repurposing_Therapeutics_for_the_Wuhan_Coronavirus_nCov-2019_Supercomputer-Based_Docking_to_the_Viral_S_Protein_and_Human_ACE2_Interface/11871402/3
======
turkeytotal
Abstract:

 _The novel Wuhan coronavirus (SARS-CoV-2) has been sequenced, and the virus
shares substantial similarity with SARS-CoV. Here, using a computational model
of the spike protein (S-protein) of SARS-CoV-2 interacting with the human ACE2
receptor, we make use of the world 's most powerful supercomputer, SUMMIT, to
enact an ensemble docking virtual high-throughput screening campaign and
identify small-molecules which bind to either the isolated Viral S-protein at
its host receptor region or to the S protein-human ACE2 interface. We
hypothesize the identified small-molecules may be repurposed to limit viral
recognition of host cells and/or disrupt host-virus interactions. A ranked
list of compounds is given that can be tested experimentally_

Additional snippet:

 _Here we combine restrained temperature replica-exchangemolecular dynamics
(restrained T-REMD) simulations with virtual high-throughput screening in an
ensemble docking campaign to identify well-characterized drugs, metabolites,
and /or natural products that may disrupt S-protein:ACE2 receptor interface
stability or the ability of the S-protein to recognize the ACE2 receptor. From
this ensemble docking campaign,we provide a ranking of the predicted binding
affinities ofover 8000 drugs, metabolites, and natural products (and their
isomers)with regards to the COVID-19 S-protein and the S-protein:ACE2
receptor. Further, we highlight seven of our top ranked compounds, which are
currently available and have had either regulatory approval as drugs or have
had multiple prior studies which indicating high-potential for therapeuticuse_

