SUBMISSION &
DATA COLLECTION
of the crowdsourced simulations
18 weeks
You have the opportunity to get a GPU WORKSTATION equipped with an OCULUS QUEST 2 virtual reality headset.
Make your Molecular Docking studies with our protein/ligands dataset. Suggest a set of molecules (up to 15) among those screened.
We WILL PURCHASE them for you and EXPERIMENTALLY TEST them.
In addition to the viral proteins, we will also providing X-ray sets of HUMAN HOST PROTEIN structures.
EXSCALATE4COV project offers you CPU/GPU hours on the
CINECA super computer infrastructure and a special issue on the International Journal of Molecular Sciences (ISSN 1422-0067) to quickly share your results.
of the crowdsourced simulations
18 weeks
Generation of a single Final Ranking by using
ML and AI technologies thanks to the SAS platform
6 weeks
Purchase of the best candidates
selected in phase 2
6 weeks
The libraries will be tested
in all our COVID19 assay and the in all our EXSCALATE4COV assay and
the most promising could be crystallized
8 weeks
Results on the compounds will be published
in public portals and make available
2 weeks
MEDIATE project put at your disposal the VIRAL PROTEINS with the higher pharmaceutical interest and the BINDING SITES identified with our method recently published in the International Journal of Molecular Sciences. (for more details www.mdpi.com )
This novel strategy for pocket mapping, based on the combination of pocket and docking searches is proved successful in precisely characterizing a set of SARS-CoV-2 druggable binding pockets including both orthosteric and allosteric sites, which will be very useful for your MEDIATE virtual screening campaign.
All compounds were converted to 3D and prepared with Schrödinger’s LigPrep tool (Schrödinger Release 2020-2: LigPrep, Schrödinger, LLC, New York, NY, 2020.). This process generated multiple states for stereoisomers, tautomers, ring conformations (1 stable ring conformer by default) and protonation states. The Schrödinger package Epik was used to assign tautomers and protonation states that would be dominant at a selected pH range (pH=7±1).
Ambiguous chiral centers were enumerated, allowing a maximum of 32 isomers to be produced from each input structure. Then, an energy minimization was performed with the OPLS3 force field ([Harder2016]). Duplicates among the libraries were removed.
Protein | Compound | Dock Score |
---|---|---|
3CL-PRO | 1000399 | 0.99 |
N-PROTEIN | 1000866 | 0.98 |
NSP12-NSP7-NSP8 | 10063 | 0.52 |
SPIKE-ACE2 | 1006305 | 0.12 |