Quantum study of mutational effect in binding of efavirenz to HIV-1 RT.
Full quantum mechanical computational study has been carried out to study binding of efavirenz (EFZ), a second generation FDA approved nonnucleoside inhibitor, to HIV-1 reverse transcriptase (RT) and its K103N and Y181C mutants using the MFCC (molecular fractionation with conjugate caps) method. The binding interaction energies between EFZ and each protein fragment are calculated using a combination of HF/3-21G, B3LYP/6-31G* and MP2/6-31G* ab initio levels. The present computation shows that Efavirenz binds to HIV-1 RT predominantly through strong electrostatic interaction with the Lys101 residue. The small loss of binding to K103N mutant by Efavirenz can be attributed to a slightly weakened attractive interaction between the drug and Lys101 due to a conformational change of mutation. The small loss of binding to Y181C mutant by efavirenz can be attributed to the Glu698 residue moving closer to EFZ due to conformational change, which results in an increase of repulsive energy relative to the wild type (WT). The binding of efavirenz-derived DPC961 to HIV-1 RT is enhanced by an additional attractive interaction to residue Hid235 and reduced repulsion to Glu698, resulting in an increase of binding energy by about 4 kcal/mol.
Mei
Ye
Y
Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, College of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
He
Xiao
X
Xiang
Yun
Y
Zhang
Da W
DW
Zhang
J Z H
JZ
D000480:Alkynes; D048588:Benzoxazines; D001665:Binding Sites; D003521:Cyclopropanes; D054303:HIV Reverse Transcriptase / Q000737:chemistry / Q000378:metabolism*; D015497:HIV-1 / Q000201:enzymology*; D008239:Lysine; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D009153:Mutagens / Q000493:pharmacokinetics*; D010078:Oxazines / Q000737:chemistry / Q000493:pharmacokinetics*; D010446:Peptide Fragments / Q000737:chemistry; D011485:Protein Binding; D011789:Quantum Theory; D018894:Reverse Transcriptase Inhibitors / Q000737:chemistry / Q000493:pharmacokinetics*; D013816:Thermodynamics
D000480:Alkynes; D048588:Benzoxazines; D003521:Cyclopropanes; D009153:Mutagens; D010078:Oxazines; D010446:Peptide Fragments; D018894:Reverse Transcriptase Inhibitors; D054303:HIV Reverse Transcriptase; C098320:efavirenz; D008239:Lysine