Analysis of the domain interactions between the protease and helicase of NS3 in dengue and hepatitis C virus

Rosales-León, Luis; Ortega-Lule, G.; Ruíz-Ordaz, Blanca H.

doi:10.1016/j.jmgm.2006.04.001

Cited by 7 publications

(5 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similarly, Ganesh et al, in 2005 [59], and Tomlinson et al, in 2009 [26], used homology models based on the retracted structure for automatic docking studies. For studying the importance of domain motion between the NS3 PRO and NS3 HEL domains through MD simulations (1 ns), Rosales-León et al, in 2007 [66], built a full DENV NS3 model, but also based on this retracted structure. In 2010, two groups [29,67] independently published a similar approach for building active conformational models, where the cofactor and the ligand were extracted from the WNV NS2B CF /NS3 PRO structure (PDB id 2FP7) and fused to the DENV NS3 PRO .…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2013

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

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

et al. 2013

View full text Add to dashboard Cite

show abstract

“…The interdomain (linker) region 169–179 and the two loops that encircle the entrance of the ATP binding pocket of NS3 [ 31 ] were also studied because of the role of this protein in virus replication. This region has also been implicated in the intrinsic flexibility required to couple movements between the NS3 protease and helicase domains [ 31 , 32 ]. We found no change in these amino acids.…”

Section: Discussionmentioning

confidence: 99%

Specific genetic markers for detecting subtypes of dengue virus serotype-2 in isolates from the states of Oaxaca and Veracruz, Mexico

et al. 2008

View full text Add to dashboard Cite

Background: Dengue (DEN) is an infectious disease caused by the DEN virus (DENV), which belongs to the Flavivirus genus in the family Flaviviridae. It has a (+) sense RNA genome and is mainly transmitted to humans by the vector mosquito Aedes aegypti. Dengue fever (DF) and dengue hemorrhagic fever (DHF) are caused by one of four closely related virus serotypes (DENV-1, DENV-2, DENV-3 and DENV-4). Epidemiological and evolutionary studies have indicated that host and viral factors are involved in determining disease outcome and have proved the importance of viral genotype in causing severe epidemics. Host immune status and mosquito vectorial capacity are also important influences on the severity of infection. Therefore, an understanding of the relationship between virus variants with altered amino acids and high pathogenicity will provide more information on the molecular epidemiology of DEN. Accordingly, knowledge of the DENV serotypes and genotypes circulating in the latest DEN outbreaks around the world, including Mexico, will contribute to understanding DEN infections.

show abstract

“…The substrate DNA was generated by annealing an 18-base 32 P-labeled and an unlabelled 28-base oligonucleotide, creating a duplex substrate with a 3’-ssDNA overhang (required for helicase recognition and activity (Kuang et al, 2004; Lam et al, 2003; Rosales-Leon et al, 2007). The reaction consisted of 1nM dsDNA substrate and 20nM HCV helicase incubated in reaction buffer (25mM MOPS, pH6.5, 3mM MgCl 2 , 0.1% Tween 20) for 30 min at 37°C.…”

Section: Experimental Methodsmentioning

confidence: 99%

Mutations in HCV non-structural genes do not contribute to resistance to nitazoxanide in replicon-containing cells

et al. 2011

View full text Add to dashboard Cite

Nitazoxanide(NTZ) exhibits potent antiviral activity against hepatitis C virus (HCV) in cell culture. Previously, HCV replicon-containing cell lines resistant to NTZ were selected, but transfer the HCV NTZ-resistance phenotype was not observed following transfection of whole cell RNA. To further explore the nature of the resistance of HCV to NTZ, full length HCV replicon sequences were obtained from two NTZ-resistant (NTZ-11, TIZ-9), and the parental (RP7) cell lines. Numerous nucleotide changes were observed in individual HCV genomes relative to the RP7 HCV consensus sequence, but no common mutations in the HCV nonstructural genes or 3’-UTRwere detected. A cluster of single nucleotide mutations was found within a 5-base portion of the 5’-UTR in 20/21 HCV replicon sequences from both resistant cell lines. Three mutations (5’-UTR G17A, G18A, C20U) were individually inserted into CON1 (‘wild-type’) HCV replicons, showed reduced replication (5 to 50-fold), but none conferred resistance to NTZ. RP7, NTZ-11, and TIZ-9 were cured of HCV genomes by serial passage under interferon. Transfection of cured NTZ-11 and TIZ-9 with either whole cell RNAs from RP7, NTZ-11, or TIZ-9, ‘wild-type’ or the 5’-UTR mutation-containing replicon RNAsexhibited an NTZ-resistance phenotype. TIZ (the active metabolite of NTZ) was found to be inactive against the activity of HCV polymerase, protease, and helicase in enzymatic assays. These data confirm previous speculations that HCV resistance to NTZ is not due to mutations in the virus, and demonstrate that HCV resistance and most likely the antiviral activity of TIZ are due to interactions with cellular target(s).

show abstract

Analysis of the domain interactions between the protease and helicase of NS3 in dengue and hepatitis C virus

Cited by 7 publications

References 41 publications

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

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

Specific genetic markers for detecting subtypes of dengue virus serotype-2 in isolates from the states of Oaxaca and Veracruz, Mexico

Mutations in HCV non-structural genes do not contribute to resistance to nitazoxanide in replicon-containing cells

Contact Info

Product

Resources

About