Tripeptide inhibitors of dengue and West Nile virus NS2B–NS3 protease

Schüller, Andreas; Yin, Zheng; Chia, C. S. Brian; Doan, Danny N.P.; Kim, Hyeong-Kyu; Shang, Luqing; Loh, Teck Peng; Hill, Jeffery; Vasudevan, Subhash G.

doi:10.1016/j.antiviral.2011.07.002

Cited by 85 publications

(65 citation statements)

References 18 publications

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“…Aprotinin is a potent inhibitor of both WNV and DENV proteases, with a greater activity against DENV (21). In contrast, peptides typically show better potency against WNV protease than DENV protease (27). These results are in agreement with the observations that DENV protease with NS2B in the open conformation binds readily to aprotinin but needs to be induced to a closed conformation to bind peptide inhibitors.…”

Section: Discussionsupporting

confidence: 82%

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Ligand-Bound Structures of the Dengue Virus Protease Reveal the Active Conformation

Noble

Seh

Chao

et al. 2012

J Virol

251

385

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Dengue is a mosquito-borne viral hemorrhagic disease that is a major threat to human health in tropical and subtropical regions. Here we report crystal structures of a peptide covalently bound to dengue virus serotype 3 (DENV-3) protease as well as the serine-protease inhibitor aprotinin bound to the same enzyme. These structures reveal, for the first time, a catalytically active, closed conformation of the DENV protease. In the presence of the peptide, the DENV-3 protease forms the closed conformation in which the hydrophilic ␤-hairpin region of NS2B wraps around the NS3 protease core, in a manner analogous to the structure of West Nile virus (WNV) protease. Our results confirm that flavivirus proteases form the closed conformation during proteolysis, as previously proposed for WNV. The current DENV-3 protease structures reveal the detailed interactions at the P4= to P3 sites of the substrate. The new structural information explains the sequence preference, particularly for long basic residues in the nonprime side, as well as the difference in substrate specificity between the WNV and DENV proteases at the prime side. Structural analysis of the DENV-3 protease-peptide complex revealed a pocket that is formed by residues from NS2B and NS3; this pocket also exists in the WNV NS2B/NS3 protease structure and could be targeted for potential antivirus development. The structural information presented in the current study is invaluable for the design of specific inhibitors of DENV protease. Dengue virus (DENV) is a member of the flavivirus genus, which includes several viruses that are important human pathogens, including yellow fever virus (YFV), Japanese encephalitis virus (JEV), West Nile virus (WNV), and tick-borne encephalitis virus (TBEV). The four serotypes of DENV are estimated to cause 50 to 100 million human infections worldwide every year in tropical and subtropical regions (16). There are currently no clinically approved vaccines or therapeutics for DENV. Understanding the molecular details of DENV infection is essential for vaccine and antiviral development.Flaviviruses contain a single strand of positive-sense RNA that encodes three structural and seven nonstructural (NS) proteins that are translated as a single polypeptide chain. NS3 contains two functions, an N-terminal serine protease and a C-terminal RNA helicase. The catalytic triad (His51, Asp75, and Ser135) is within the NS3 protease domain, but a region of NS2B is also required for catalytic activity (15). NS2B contains three predicted transmembrane helices, ensuring that the NS2B-NS3 protease is bound to the endoplasmic reticulum. The viral polyprotein is cleaved into the individual proteins by a combination of host proteases and the viral NS2B-NS3 protease (6, 30). The proteolytic activity of the viral protease is essential for viral replication, making it an excellent antiviral target (18).Ligand-free structures of flavivirus proteases have been solved for DENV-1 and -2 and a WNV active-site mutant (1, 7, 13). In addition, the structure of Mur...

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Section: Discussionsupporting

confidence: 82%

“…This probably explains why similar peptides are typically Ͼ10-fold more potent inhibitors of WNV than DENV proteases (27). It also explains why previous attempts to crystallize DENV protease with bound inhibitors have been unsuccessful.…”

Section: Discussionmentioning

confidence: 82%

Ligand-Bound Structures of the Dengue Virus Protease Reveal the Active Conformation

Noble

Seh

Chao

et al. 2012

J Virol

251

385

View full text Add to dashboard Cite

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“…Much effort has been invested into screening for DENV protease inhibitors as potential drug targets (33)(34)(35)(36)(37)(38)(39)(40)(41). The linked DENV protease construct has been widely utilized for in vitro biochemical assays and in silico compound screening.…”

Section: Discussionmentioning

confidence: 99%

NMR Analysis of a Novel Enzymatically Active Unlinked Dengue NS2B-NS3 Protease Complex

Kim

Gayen

Kang

et al. 2013

Journal of Biological Chemistry

102

178

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Background: Dengue protease is a two-component protease that is important for viral replication. Results: An unlinked protease complex containing the NS2B regulatory region and the NS3 protease domain was obtained. Conclusion:The unlinked protease complex produces dispersed cross-peaks in NMR spectra and exists predominantly in a closed conformation in solution.Significance: This new construct will be a useful tool for drug discovery against the dengue virus.

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“…This scenario could explain the relatively low success of previous virtual screening attempts against this target. In fact, the flexibility of DENV NS2B/NS3 protease has already been proposed, but not proved, to explain the poor results of current drug design campaigns [21]. …”

Section: Introductionmentioning

confidence: 99%

New Binding Site Conformations of the Dengue Virus NS3 Protease Accessed by Molecular Dynamics Simulation

et al. 2013

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Dengue fever is caused by four distinct serotypes of the dengue virus (DENV1-4), and is estimated to affect over 500 million people every year. Presently, there are no vaccines or antiviral treatments for this disease. Among the possible targets to fight dengue fever is the viral NS3 protease (NS3PRO), which is in part responsible for viral processing and replication. It is now widely recognized that virtual screening campaigns should consider the flexibility of target protein by using multiple active conformational states. The flexibility of the DENV NS3PRO could explain the relatively low success of previous virtual screening studies. In this first work, we explore the DENV NS3PRO conformational states obtained from molecular dynamics (MD) simulations to take into account protease flexibility during the virtual screening/docking process. To do so, we built a full NS3PRO model by multiple template homology modeling. The model comprised the NS2B cofactor (essential to the NS3PRO activation), a glycine flexible link and the proteolytic domain. MD simulations had the purpose to sample, as closely as possible, the ligand binding site conformational landscape prior to inhibitor binding. The obtained conformational MD sample was clustered into four families that, together with principal component analysis of the trajectory, demonstrated protein flexibility. These results allowed the description of multiple binding modes for the Bz-Nle-Lys–Arg–Arg-H inhibitor, as verified by binding plots and pair interaction analysis. This study allowed us to tackle protein flexibility in our virtual screening campaign against the dengue virus NS3 protease.

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Tripeptide inhibitors of dengue and West Nile virus NS2B–NS3 protease

Cited by 85 publications

References 18 publications

Ligand-Bound Structures of the Dengue Virus Protease Reveal the Active Conformation

Ligand-Bound Structures of the Dengue Virus Protease Reveal the Active Conformation

NMR Analysis of a Novel Enzymatically Active Unlinked Dengue NS2B-NS3 Protease Complex

New Binding Site Conformations of the Dengue Virus NS3 Protease Accessed by Molecular Dynamics Simulation

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