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Flap Dynamics in Aspartic Proteases: A Computational Perspective
Author(s) -
Mahanti Mukul,
Bhakat Soumendranath,
Nilsson Ulf J.,
Söderhjelm Pär
Publication year - 2016
Publication title -
chemical biology and drug design
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.59
H-Index - 77
eISSN - 1747-0285
pISSN - 1747-0277
DOI - 10.1111/cbdd.12745
Subject(s) - proteases , metadynamics , molecular dynamics , computational biology , ligand (biochemistry) , chemistry , molecular mechanics , computer science , biophysics , biology , biochemistry , computational chemistry , enzyme , receptor
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.