Document Detail


Structural and energetic analysis on the complexes of clinically isolated subtype C HIV-1 proteases and approved inhibitors by molecular dynamics simulation.
MedLine Citation:
PMID:  20055526     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
HIV-1 has a large genetic diversity. Subtype B HIV-1 is commonly found in patients in developed countries. In contrast, an increasing number of patients are infected with the non-B subtype viruses, especially with subtype C HIV-1, in developing countries. It remains to be clarified how mutations or polymorphisms in non-B subtype HIV-1 influence the efficacy of the approved inhibitors. In this study, we have performed molecular dynamics simulations on clinically isolated subtype C HIV-1 proteases in complex with three kinds of approved inhibitors. From the structural and energetic viewpoints, we identified the polymorphisms influencing on the binding of the inhibitors. The effect of the V82I mutation on the association with chemicals and the reason for rare appearance of the D30N mutation in subtype C HIV-1 were discussed in terms of the change of geometry of the residues in HIV-1 protease.
Authors:
Shou Matsuyama; Ay Aydan; Hirotaka Ode; Masayuki Hata; Wataru Sugiura; Tyuji Hoshino
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  The journal of physical chemistry. B     Volume:  114     ISSN:  1520-5207     ISO Abbreviation:  J Phys Chem B     Publication Date:  2010 Jan 
Date Detail:
Created Date:  2010-01-08     Completed Date:  2010-03-12     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101157530     Medline TA:  J Phys Chem B     Country:  United States    
Other Details:
Languages:  eng     Pagination:  521-30     Citation Subset:  IM    
Affiliation:
Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan.
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Substitution
Anti-HIV Agents / chemistry*,  pharmacology
Genetic Variation
HIV Protease / chemistry*,  metabolism
HIV Protease Inhibitors / chemistry*,  pharmacology
Humans
Hydrogen Bonding
Molecular Dynamics Simulation
Mutation
Thermodynamics
Chemical
Reg. No./Substance:
0/Anti-HIV Agents; 0/HIV Protease Inhibitors; EC 3.4.23.-/HIV Protease; EC 3.4.23.-/p16 protease, Human immunodeficiency virus 1

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