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Conformational flexibility of DENV NS2B/NS3pro: from the inhibitor effect to the serotype influence

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Abstract

The dengue virus (DENV) has four well-known serotypes, namely DENV1 to DENV4, which together cause 50–100 million infections worldwide each year. DENV NS2B/NS3pro is a protease recognized as a valid target for DENV antiviral drug discovery. However, NS2B/NS3pro conformational flexibility, involving in particular the NS2B region, is not yet completely understood and, hence, a big challenge for any virtual screening (VS) campaign. Molecular dynamics (MD) simulations were performed in this study to explore the DENV3 NS2B/NS3pro binding-site flexibility and obtain guidelines for further VS studies. MD simulations were done with and without the Bz-nKRR-H inhibitor, showing that the NS2B region stays close to the NS3pro core even in the ligand-free structure. Binding-site conformational states obtained from the simulations were clustered and further analysed using GRID/PCA, identifying four conformations of potential importance for VS studies. A virtual screening applied to a set of 31 peptide-based DENV NS2B/NS3pro inhibitors, taken from literature, illustrated that selective alternative pharmacophore models can be constructed based on conformations derived from MD simulations. For the first time, the NS2B/NS3pro binding-site flexibility was evaluated for all DENV serotypes using homology models followed by MD simulations. Interestingly, the number of NS2B/NS3pro conformational states differed depending on the serotype. Binding-site differences could be identified that may be crucial to subsequent VS studies.

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Abbreviations

2D-RMSD:

Two-dimensional root-mean-square deviations

Bz-nKRR-H:

Benzoyl-norleucine-lysine-arginine-arginine-aldehyde

DENV:

Dengue virus

DENV1:

Dengue virus serotype 1

DENV2:

Dengue virus serotype 2

DENV3:

Dengue virus serotype 3

DENV4:

Dengue virus serotype 4

DHF:

Dengue haemorrhagic fever

DSS:

Dengue shock syndrome

H-bond:

Hydrogen bond

Ki :

Inhibition constant

MIFs:

Molecular interactions fields

MD:

Molecular dynamics

NMR:

Nuclear magnetic resonance

NS2B:

Non-structural protein 2B

NS3pro:

Protease domain of non-structural protein 3

PC:

Principal component

PCA:

Principal component analyses

PDB:

Protein data bank

RMSD:

Root-mean-square deviations

RMSF:

Root-mean-square fluctuations

VS:

Virtual screening

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Acknowledgments

This study was supported by grants of Fundação de Amparo à Pesquisa no Estado de São Paulo (FAPESP), Brazil, and of Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil. A.T-do A. is member of the CEPID Redoxoma (No. 2013/07937-8) and of the NAP Redoxoma (PRPUSP). E.P. was recipient of PhD studentships from FAPESP (No. 2014/01614-5 and No.2012/06633-2). A.T-do A. was recipient of fellowship from CNPq (No. 305809/2012-1).

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Authors and Affiliations

  1. Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil

    Erika Piccirillo & Antonia T. do Amaral

  2. Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany

    Benjamin Merget & Christoph A. Sotriffer

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  1. Erika Piccirillo
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  2. Benjamin Merget
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  3. Christoph A. Sotriffer
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  4. Antonia T. do Amaral
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Correspondence to Antonia T. do Amaral.

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Piccirillo, E., Merget, B., Sotriffer, C.A. et al. Conformational flexibility of DENV NS2B/NS3pro: from the inhibitor effect to the serotype influence. J Comput Aided Mol Des 30, 251–270 (2016). https://doi.org/10.1007/s10822-016-9901-8

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