4CTJ

DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-ADENOSYL METHIONINE AND FRAGMENT 3A9

Summary for 4CTJ

• Entry DOI: 10.2210/pdb4ctj/pdb
• Related: 4CTK
• Descriptor: NON-STRUCTURAL PROTEIN 5, S-ADENOSYLMETHIONINE, 2,3-dihydro-1-benzofuran-5-carboxylic acid, ... (5 entities in total)
• Functional Keywords: transferase, ns5 methyltransferase, fragment-based drug discovery, antiviral screening
• Biological source: DENGUE VIRUS 3
• Cellular location: Virion membrane; Multi-pass membrane protein: A9LIE0
• Total number of polymer chains: 2
• Total formula weight: 63397.65

Authors

Barral, K.,Bricogne, G.,Sharff, A. (deposition date: 2014-03-14, release date: 2014-04-16, Last modification date: 2024-05-08)

Primary citation

Coutard, B.,Decroly, E.,Li, C.,Sharff, A.,Lescar, J.,Bricogne, G.,Barral, K.
Assessment of Dengue Virus Helicase and Methyltransferase as Targets for Fragment-Based Drug Discovery.
Antiviral Res., 106:61-, 2014

PubMed Abstract: Seasonal and pandemic flaviviruses continue to be leading global health concerns. With the view to help drug discovery against Dengue virus (DENV), a fragment-based experimental approach was applied to identify small molecule ligands targeting two main components of the flavivirus replication complex: the NS3 helicase (Hel) and the NS5 mRNA methyltransferase (MTase) domains. A library of 500 drug-like fragments was first screened by thermal-shift assay (TSA) leading to the identification of 36 and 32 fragment hits binding Hel and MTase from DENV, respectively. In a second stage, we set up a fragment-based X-ray crystallographic screening (FBS-X) in order to provide both validated fragment hits and structural binding information. No fragment hit was confirmed for DENV Hel. In contrast, a total of seven fragments were identified as DENV MTase binders and structures of MTase-fragment hit complexes were solved at resolution at least 2.0Å or better. All fragment hits identified contain either a five- or six-membered aromatic ring or both, and three novel binding sites were located on the MTase. To further characterize the fragment hits identified by TSA and FBS-X, we performed enzymatic assays to assess their inhibition effect on the N7- and 2'-O-MTase enzymatic activities: five of these fragment hits inhibit at least one of the two activities with IC50 ranging from 180μM to 9mM. This work validates the FBS-X strategy for identifying new anti-flaviviral hits targeting MTase, while Hel might not be an amenable target for fragment-based drug discovery (FBDD). This approach proved to be a fast and efficient screening method for FBDD target validation and discovery of starting hits for the development of higher affinity molecules that bind to novel allosteric sites.

PubMed: 24704437
DOI: 10.1016/J.ANTIVIRAL.2014.03.013

Experimental method

X-RAY DIFFRACTION (1.47 Å)