MEDIATE
MolEcular DockIng AT homE

You find them. We test them. Together we defeat COVID-19.

Arieh Warshel

Arieh Warshel

Nobel Laureate, 2013 Chemistry Distinguished Professor of Chemistry and Biology at the University of Southern California (USA)

Igor V. Tetko

Igor V. Tetko

Chemoinformatics Group Leader Helmholtz Zentrum München (Germany)

Rossen Apostolov

Rossen Apostolov

Executive Director at BioExCel Center of Excellence for Computational Biomolecular Research

Yang Ye

Yang Ye

Full professor and deputy director of the Shanghai Institute of Materia Medica, Chinese Academy of Sciences.

You can really make the difference!

Deadline for submission to be announced

REGISTRATION

Sign up your team and get the access toour LIGANDS and PROTEINS Libraries   

GET YOUR VIRTUAL REALITY
WORK STATION!

You have the opportunity to get a GPU WORKSTATION equipped with an OCULUS QUEST 2 virtual reality headset.   

SUGGEST YOUR BEST MOLECULES

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.  

NEW PROTEIN STRUCTURES

In addition to the viral proteins, we will also providing X-ray sets of HUMAN HOST PROTEIN structures.  

10M HOURS OF CALCULATIONS
@CINECA HPC CENTER

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.  

THE MEDIATE PROJECT

We want to collect the BEST POSSIBLE CHEMICAL LIBRARY of NOVEL INHIBITORS OF SARS-COV-2 targeting the most relevant viral proteins combining as much as possible VIRTUAL SCREENING SIMULATIONS and AI PREDICTIONS generated by THE BEST DRUG HUNTERS WORLDWIDE.

THE MEDIATE INITIATIVE IS PART OF THE EXSCALATE4COV PROJECT

E4C is the public-private consortium backed by the European Commission’s H2020 program. It currently represents the most advanced center of competence aimed at fighting the coronavirus by combining the best supercomputing resources and artificial intelligence with state of the art experimental facilities up through clinical validation.

In June 2020, E4C announced that an already registered generic drug used to treat osteoporosis (Raloxifene) could be effective in treating COVID-19 patients with mild symptoms of infection.

ACTIONS

How to participate to the Covid-19 MEDIATE?

1

SUBMISSION &
DATA COLLECTION

of the crowdsourced simulations


 18 weeks 

2

COMPOUNDS SELECTION

Generation of a single Final Ranking by using
ML and AI technologies thanks to the SAS platform 

6 weeks 

3

COMPOUNDS ACQUISITION

Purchase of the best candidates
selected in phase 2 

6 weeks  

4

TESTING

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 

5

DATA SHARING

Results on the compounds will be published
in public portals and make available 


2 weeks 

THE MEDIATE PROJECT

SAS

STRUCTURAL DATA

The TARGETS

 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.

The LIGANDS

 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.

RESULTS

The compounds with the best scores, selected from your valuable Molecular Docking simulations, will be tested by us in BIOCHEMICAL and CELLULAR SCREENING to evaluate their real effectiveness.

Together, we will transform VIRTUAL results into CONCRETE data!

BEST SCORED ligands screened on VIRAL PROTEINS so far

Protein Compound Dock Score
3CL-PRO10003990.99
N-PROTEIN10008660.98
NSP12-NSP7-NSP8100630.52
SPIKE-ACE210063050.12
showing 4 results  out of
Address

Excalate4Cov
c/o Dompé Farmaceutici
Via Pietro Castellino, 111
80131 Napoli, Italy

Contacts

Email:  info@exscalate4cov.eu