Participants :
AMU,Uzl,LUMC,Institut Pasteur,UKL-HD,Riboxx,Oxford University,

Antiviral targets in complex with RNA and inhibitors

Type of activity : RTD (Research and technological development including scientific coordination – applicable for collaborative projects and NoEs,).
Lead beneficiary : AMU/AFMB.
Person-months : 699
Start month : 1
End month : 48

Objectives :

RNA virus replicases adopt widely different conformations upon binding to their RNA substrates. The lack of crystal structures of RNA/replicase complexes is hampering not only structure-based drug design but also mechanism-of-action and drug-resistance studies. WP2 aims to provide the best structural description of viral targets in complex with RNA and relevant substrates/inhibitors. To achieve this, we will employ the most appropriate technology to produce high concentrations of biologically relevant RNA substrates in large quantity (task 2.1). and deliver them to the relevant target-driven tasks. Selected viral enzymes will be crystallized in complex with these RNA substrates and both uninhibited and inhibited complexes will be mechanistically characterized (tasks 2.1-2.5, and with WP3). Major effort will be put on protein of SILVER’s three priority virus groups, dengue viruses (task 2.3), viruses in the family Picornaviridae (task 2.4), and Paramyxoviruses (task 2.5). Other selected viral enzymes will enter the pipeline at an earlier stage, to advance knowledge and technical know-how towards hit discovery (task 2.6). Defined and relevant RNA substrates will be selected through bioinformatics analysis, (P1b, 9, 11, 12), synthesized chemically (P11) and/or enzymatically (P1b), optimized in sequence, size and binding affinity, produced and purified in large scale (P1b, 9, 11), and used in co-crystallization experiments (P1b, 12, 13). Crystal structures of complexes will be determined in the presence and absence of inhibitors, in close collaboration with WP3. Differential activities and activity levels between liganded and unliganded enzymes (RNA, activators, inhibitors, cosubstrates) will be studied in detail (P1b, 2, 4, 7, 12, 13) in order to determine unambiguously the inhibited form/conformation of the viral target and deliver a sound mechanism-of-action.

Description :
Combination of protein expression with RNA synthesis to explore novel large-scale methods of protein RNA complex formation and purification .

The research leading to these results has received funding from the European Union Seventh Programme (FP7 2007/2013) under grant agreement n°260644-SILVER