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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Comparison of the Molecular Dynamics and Calculated Binding Free Energies for Nine FDA-Approved HIV-1 PR Drugs Against Subtype B and C-SA HIV PR
Chemical Biology and Drug Design, Volume 81, No. 2, Year 2013
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Description
We report the first account of a comparative analysis of the binding affinities of nine FDA-approved drugs against subtype B as well as the South African subtype C HIV PR (C-SA). A standardized protocol was used to generate the inhibitor/C-SA PR complexes with the relative positions of the inhibitors taken from the corresponding X-ray structures for subtype B complexes. The dynamics and stability of these complexes were investigated using molecular dynamics calculations. Average relative binding free energies for these inhibitors were calculated from the molecular dynamics simulation using the molecular mechanics generalized Born surface area method. The calculated energies followed a similar trend to the reported experimental binding free energies. Postdynamic hydrogen bonding and electrostatic interaction analysis of the inhibitors with both subtypes reveal similar interactions. Most inhibitors show slightly weaker binding affinities for C-SA PR. Molecular dynamics studies demonstrated increased flap movement for C-SA PR, which can perhaps explain the weaker affinities. This study serves as a standardized platform for optimizing the design of future more potent HIV C-SA PR inhibitors. © 2012 John Wiley & Sons A/S.
Authors & Co-Authors
Ahmed, Shaimaa M.
South Africa, Durban
University of Kwazulu-natal
Kruger, Hendrik G.
South Africa, Durban
University of Kwazulu-natal
Govender, Thirumala
South Africa, Durban
University of Kwazulu-natal
Maguire, Glenn E.M.
South Africa, Durban
University of Kwazulu-natal
Sayed, Yasien
South Africa, Johannesburg
University of the Witwatersrand
Ibrahim, Mahmoud A.A.
United Kingdom, Manchester
The University of Manchester
Egypt, Minya
Faculty of Science
Naicker, Previn
South Africa, Johannesburg
University of the Witwatersrand
Soliman, Mahmoud E.S.
South Africa, Durban
University of Kwazulu-natal
Egypt, Zagazig
Faculty of Pharmacy
Statistics
Citations: 40
Authors: 8
Affiliations: 5
Identifiers
Doi:
10.1111/cbdd.12063
ISSN:
17470277
e-ISSN:
17470285
Research Areas
Infectious Diseases