Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants to BI201335

Supervisor: Richard Hsung Professor ,Dr. Wei Jing Student: Fu JianjianSubject: Pharmaceutical chemistry

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Experimental plan

Topic schedule implementation scheme

References5

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Outline

1 Introduction to research topics

2

2 Current research situation at home and abroad

1 Introduction to my research

• HCV is a serious and growing threat to human health– HCV NS3/4A serine protease is a trypsin-like protease essential

for RNA replication.--- Drug resistance of HCV NS3/4A protease often occurs to its

inhibitors. – BI201335 , a competitive inhibitor contains a unique C-terminal

carboxylic acid that binds noncovalently to the active site is in phase3 of clinical trials,which is devoleped by Boehringer Ingelheim incoportion

– To data,there have not any report to the drug resistant mechanism research to BI201335

1 Introduction to my research

MethodMethod ObjectiveObjective

Contents

Contents

Structural change responsible for the drug resistance

Energetic changes responsible for drug resistance

Research method and objective

Description of the contents Description of the contents

Using the molecular dynamics simulations,when the complex isstable, calculate the binding free energy analyse the xianghuzuo Yong between the protease and the inhibitor

1 Introduction to my research

2)May be critical for the development of novel inhibitors that are less susceptible to drug

resistance.

Significance of the topic

1)provide some insights into the resistance mechanism of NS3/4A protease mutants to

BI201335

2 Current research situation at home and abroad

The molecular dynamics is widely used to evaluate the drug resistance mechanism in HIV drugs and anti-cancer drugs.

1 Chunli Yan,Comparative molecular dynamics simulations of histone deacetylase-like protein:Binding hydroxamic acid inhibitors.Proteins.2009,73(1):134-147.

2 GU HUI et al.Molecular dynamics simulations exploring drug resistance in HIV-1 protease.Bioinformatics.2010,55(24):2677-2683.

3 Yufeng Cai et al.Differential Flap Dynamics in Wild-Type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J. Chem. Theory Comput., 2012, 8 (10): 3452–3462.

3 Experimental plan

Research contents

Step three

Content analysis

Step one

Preparation of initial

structures

Step four

Results and conclusions

Step two

Molecular dynamics simulations

Preparation of initial structures

1 Download the X-ray crystal structure of wild-type HCV NS3/4A protease complexed with BI201335

2 MOE software will be applied to generate the 3D structure of the studies mutants (eghit complexes including the wild type one) in complex with BI201335 by substituting specific residues using the wide type model as the template.

Do molecular dynamics using the Amber10.0 software package

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The general Amber force field (GAFF) used to generated the small molecular parameters

Prepare the inhibitors parameters with Antechamber module of Amber10 package..

The standard AMBER force field (ff99SB) will be used to decribe the protein parameters

0101

0303

02020404

Do molecular dynamics using the Amber10.0

software package

Molecular dynamics simulations

Content analysis

Dynamics

stability

Root-mean square Deviation (RMSD)

MM-PBSA approach

Binding free energy

Hbond and distance

Ptraj script

Decompose the

total binding energy to each residue.

Decompose energy

Results and conclusions

Text in here Text in here

2005 2008

The resistance mechanism

4 Topic schedule

2012 2013

90% 96%

35%70%

Month 3-Month 6Literature researchData reduction

Month 12–Month 3The first draft of a paper

2012

Month 11- Month 3literature reviewopening speechopening speech

Month 8-Month 11theoretical researchConstruct paperbasic framework

Month 4-Month 5final manuscriptsPrint Finisherprepare for the speech

2011 First half of 2012 Latter half of 2012 2014

2012 2014

5 References• [1] Diane Thibeault at el. Sensitivity of NS3 Serine Proteases from Hepatitis C Virus • Genotypes 2 and 3 to the Inhibitor BILN 2061. JOURNAL OF

VIROLOGY,2004,78(14)• :7352–7359• [2] Christopher T. Lemke et al.Combined X-ray, NMR, and Kinetic Analyses Reveal

Uncommon Binding Characteristics of the Hepatitis C Virus NS3-NS4A Protease Inhibitor BI 201335. The journal of biological CHEMISTRY,2011,286(13):11434 –11443.

• [3] Paul Y. Kwo.Boceprevir: a novel nonstructural 3 (NS3) protease inhibitor for the treatment of chronic hepatitis C infection. Therapeutic Advances in Gastroenterology.

• (2012) 5(3) 179 –188.• [4] Jean-Michel Pawlotsky.Therapeutic implications of hepatitis C virus resistance • to antiviral drugs. Therapeutic Advances in Gastroenterology. (2009) 2(4) 205–219.• [5] Paul Y. Kwo.Boceprevir: a novel nonstructural 3 (NS3) protease inhibitor for the

treatment of chronic hepatitis C infection. Therapeutic Advances in Gastroenterology.• (2012) 5(3) 179 –188.• [6] Chunli Yan,Comparative molecular dynamics simulations of histone deacetylase-

like protein:Binding hydroxamic acid inhibitors.Proteins.2009,73(1):134-147.

Thank You!