Abstract:
:The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap region (residues 38-58) and the active site region (residues 23-32) in HIV-1 protease contribute 63.72% of the protease to the binding of the inhibitor. In particular, the mechanisms for the interactions of key residues of these species are fully explored and analyzed. Interestingly, the regression analyses show that both CAS and BFED based on the generalized Born model yield similar results, with a correlation coefficient of 0.94. However, compared to CAS, BFED is faster and can decompose the per-residue binding free-energy contributions into backbone and side-chain contributions. The results obtained in this study are useful for studying the binding mechanism between receptor and ligand and for designing potent inhibitors that can combat diseases.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Li D,Han JG,Chen H,Li L,Zhao RN,Liu G,Duan Ydoi
10.1007/s00894-011-1205-2subject
Has Abstractpub_date
2012-05-01 00:00:00pages
1841-54issue
5eissn
1610-2940issn
0948-5023journal_volume
18pub_type
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