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Flap Dynamics in Aspartic Proteases : A Computational Perspective

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Author

Summary, in English

Recent advances in biochemistry and drug design have placed proteases as one of the critical target groups for developing novel small-molecule inhibitors. Among all proteases, aspartic proteases have gained significant attention due to their role in HIV/AIDS, malaria, Alzheimer's disease, etc. The binding cleft is covered by one or two β-hairpins (flaps) which need to be opened before a ligand can bind. After binding, the flaps close to retain the ligand in the active site. Development of computational tools has improved our understanding of flap dynamics and its role in ligand recognition. In the past decade, several computational approaches, for example molecular dynamics (MD) simulations, coarse-grained simulations, replica-exchange molecular dynamics (REMD) and metadynamics, have been used to understand flap dynamics and conformational motions associated with flap movements. This review is intended to summarize the computational progress towards understanding the flap dynamics of proteases and to be a reference for future studies in this field.

Publishing year

2016-08-01

Language

English

Pages

159-177

Publication/Series

Chemical Biology and Drug Design

Volume

88

Issue

2

Document type

Journal article review

Publisher

Wiley-Blackwell

Topic

  • Pharmaceutical Sciences
  • Biochemistry and Molecular Biology

Keywords

  • aspartic protease
  • beta amino secretase
  • flap
  • HIV protease, plasmepsin
  • molecular modelling
  • Protease

Status

Published

ISBN/ISSN/Other

  • ISSN: 1747-0285