5K5M

Co-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA Polymerase with Compound 27

Summary for 5K5M

• Entry DOI: 10.2210/pdb5k5m/pdb
• Descriptor: RNA Dependent RNA Polymerase, ZINC ION, 5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-2,4-dimethoxy-N-[(3-methoxyphenyl)sulfonyl]benzamide, ... (5 entities in total)
• Functional Keywords: rna dependent rna polymerase, dengue, hydrolase
• Biological source: Dengue virus 2
• Cellular location: Virion membrane ; Multi-pass membrane protein : B5LNH6
• Total number of polymer chains: 1
• Total formula weight: 74590.49

Authors

Arora, R.,Benson, T.E. (deposition date: 2016-05-23, release date: 2016-08-24, Last modification date: 2024-03-06)

Primary citation

Lim, S.P.,Noble, C.G.,Seh, C.C.,Soh, T.S.,El Sahili, A.,Chan, G.K.,Lescar, J.,Arora, R.,Benson, T.,Nilar, S.,Manjunatha, U.,Wan, K.F.,Dong, H.,Xie, X.,Shi, P.Y.,Yokokawa, F.
Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling.
Plos Pathog., 12:e1005737-e1005737, 2016

PubMed Abstract: Flaviviruses comprise major emerging pathogens such as dengue virus (DENV) or Zika virus (ZIKV). The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase (RdRp) domain of non-structural protein 5 (NS5). This essential enzymatic activity renders the RdRp attractive for antiviral therapy. NS5 synthesizes viral RNA via a "de novo" initiation mechanism. Crystal structures of the flavivirus RdRp revealed a "closed" conformation reminiscent of a pre-initiation state, with a well ordered priming loop that extrudes from the thumb subdomain into the dsRNA exit tunnel, close to the "GDD" active site. To-date, no allosteric pockets have been identified for the RdRp, and compound screening campaigns did not yield suitable drug candidates. Using fragment-based screening via X-ray crystallography, we found a fragment that bound to a pocket of the apo-DENV RdRp close to its active site (termed "N pocket"). Structure-guided improvements yielded DENV pan-serotype inhibitors of the RdRp de novo initiation activity with nano-molar potency that also impeded elongation activity at micro-molar concentrations. Inhibitors exhibited mixed inhibition kinetics with respect to competition with the RNA or GTP substrate. The best compounds have EC50 values of 1-2 μM against all four DENV serotypes in cell culture assays. Genome-sequencing of compound-resistant DENV replicons, identified amino acid changes that mapped to the N pocket. Since inhibitors bind at the thumb/palm interface of the RdRp, this class of compounds is proposed to hinder RdRp conformational changes during its transition from initiation to elongation. This is the first report of a class of pan-serotype and cell-active DENV RdRp inhibitors. Given the evolutionary conservation of residues lining the N pocket, these molecules offer insights to treat other serious conditions caused by flaviviruses.

PubMed: 27500641
DOI: 10.1371/journal.ppat.1005737

Experimental method

X-RAY DIFFRACTION (2.01 Å)