9AX9

Crystal Structure of Enterovirus 68 3C Protease C147A Mutant with 3B3C peptide at 2.00 Angstroms

Summary for 9AX9

• Entry DOI: 10.2210/pdb9ax9/pdb
• Descriptor: Protease 3C, 3B3C peptide (3 entities in total)
• Functional Keywords: protease, hydrolase, enterovirus, 3c protein, ev68, inhibitor, viral protein
• Biological source: Human enterovirus D68 (EV68, EV-68); More
• Total number of polymer chains: 3
• Total formula weight: 40767.26

Authors

Azzolino, V.N.,Shaqra, A.M.,Schiffer, C.A. (deposition date: 2024-03-06, release date: 2024-09-18, Last modification date: 2024-10-09)

Primary citation

Azzolino, V.N.,Shaqra, A.M.,Ali, A.,Kurt Yilmaz, N.,Schiffer, C.A.
Elucidating the Substrate Envelope of Enterovirus 68-3C Protease: Structural Basis of Specificity and Potential Resistance.
Viruses, 16:-, 2024

PubMed Abstract: Enterovirus-D68 (EV68) has emerged as a global health concern over the last decade with severe symptomatic infections resulting in long-lasting neurological deficits and death. Unfortunately, there are currently no FDA-approved antiviral drugs for EV68 or any other non-polio enterovirus. One particularly attractive class of potential drugs are small molecules inhibitors, which can target the conserved active site of EV68-3C protease. For other viral proteases, we have demonstrated that the emergence of drug resistance can be minimized by designing inhibitors that leverage the evolutionary constraints of substrate specificity. However, the structural characterization of EV68-3C protease bound to its substrates has been lacking. Here, we have determined the substrate specificity of EV68-3C protease through molecular modeling, molecular dynamics (MD) simulations, and co-crystal structures. Molecular models enabled us to successfully characterize the conserved hydrogen-bond networks between EV68-3C protease and the peptides corresponding to the viral cleavage sites. In addition, co-crystal structures we determined have revealed substrate-induced conformational changes of the protease which involved new interactions, primarily surrounding the S1 pocket. We calculated the substrate envelope, the three-dimensional consensus volume occupied by the substrates within the active site. With the elucidation of the EV68-3C protease substrate envelope, we evaluated how 3C protease inhibitors, AG7088 and SG-85, fit within the active site to predict potential resistance mutations.

PubMed: 39339895
DOI: 10.3390/v16091419

Experimental method

X-RAY DIFFRACTION (2 Å)