239
86. Świderek K, Martí S., Moliner V (2012) Theoretical studies of HIV-1 reverse transcriptase
inhibition. Phys Chem Chem Phys 14(36):12614–12624. doi:10.1039/c2cp40953d
87. Liang YH, Chen FE (2007) ONIOM DFT/PM3 calculations on the interaction between dapivirine and HIV-1 reverse transcriptase, a theoretical study. Drug Discov Ther 1(1):57–60.
88. Garrec J, Sautet P, Fleurat-Lessard P (2011) Understanding the HIV-1 protease reactivity
with DFT: what do we gain from recent functionals?. J Phys Chem B 115(26):8545–8558.
doi:10.1021/jp200565w
89. Garrec J, Cascella M, Rothlisberger U, Fleurat-Lessard P (2010) Low inhibiting power of
N … CO based peptidomimetic compounds against HIV-1 protease: insights from a QM/
MM study. J Chem Theor Comput 6(4):1369–1379. doi:10.1021/ct9004728
90. Gautier A, Pitrat D, Hasserodt J (2006) An unusual functional group interaction and its potential to reproduce steric and electrostatic features of the transition states of peptidolysis.
Bioorg Med Chem 14(11):3835–3847. doi:10.1016/j.bmc.2006.01.031
91. Waibel M, Hasserodt J (2008) Diversity-oriented synthesis of a drug-like system displaying the distinctive N → C=O interaction. J Org Chem 73(16):6119–6126. doi:10.1021/
jo800719j
92 Waibel M, Pitrat D, Hasserodt J (2009) On the inhibition of HIV-1 protease by hydrazino-ureas displaying the N → C=O interaction. Bioorg Med Chem 17(10):3671–3679.
doi:10.1016/j.bmc.2009.03.059
93. Park C, Koh JS, Son YC, Choi H, Lee CS, Choy N, Moon KY, Jung WH, Kim SC, Yoon
H (1995) Rational design of irreversible, pseudo-C2-symmetric hiv-1 protease inhibitors.
Bioorg Med Chem Lett 5(16):1843–1848. doi:10.1016/0960-894X(95)00306-E
94. Lee CS, Choy N, Park C, Choi H, Son YC, Kim S, Ok JH, Yoon H, Kim SC (1996) Design,
synthesis, and characterization of dipeptide isostere containing cis-epoxide for the irreversible inactivation of HIV protease. Bioorg Med Chem Lett 6(6):589–594. doi:10.1016/0960894X(96)00087-X
95. Choy N, Choi H, Jung WH, Kim CR, Yoon H, Kim SC, Lee TG, Koh JS (1997) Synthesis
of irreversible HIV-1 protease inhibitors containing sulfonamide and sulfone as amide bond
isosteres. Bioorg Med Chem Lett 7(20):2635–2638. doi:10.1016/S0960-894X(97)10054-3
96. Kóňa J (2008) Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease. Org Biomol Chem 6(2):359–365.
doi:10.1039/b715828a
97. Pommier Y, Johnson AA, Marchand C (2005) Integrase inhibitors to treat HIV/AIDS. Nat
Rev Drug Discov 4(3):236–248. doi:10.1038/nrd1660
98. Ingale KB, Bhatia MS (2011) HIV-1 integrase inhibitors: a review of their chemical development. Antivir Chem Chemoth 22(3):95–105. doi:10.3851/IMP1740
99. Messiaen P, Wensing AMJ, Fun A, Nijhuis M, Brusselaers N, Vandekerckhove L (2013)
Clinical use of HIV integrase inhibitors: a systematic review and meta-analysis. PloS One
8(1):e52562. doi:10.1371/journal.pone.0052562
100. Liao C, Nicklaus MC (2010) Tautomerism and magnesium chelation of HIV-1 integrase inhibitors: a theoretical study. Chem Med Chem 5(7):1053–1066. doi:10.1002/
cmdc.201000039
101. Agrawal A, DeSoto J, Fullagar JL, Maddali K, Rostami S, Richman DD, Pommier Y, Cohen SM (2012) Probing chelation motifs in HIV integrase inhibitors. Proc Nat Acad Sci
U S A 109(7):2251–2256. doi:10.1073/pnas.1112389109
102. Thalheim T, Vollmer A, Ebert R-U, Kühne R, Schüürmann G (2010) Tautomer identification and tautomer structure generation based on the InChI code. J Chem Inf Model
50(7):1223–1232. doi:10.1021/ci1001179
103. Nunthaboot N, Pianwanit S, Parasuk V, Kokpol S, Wolschann P (2007) Theoretical study
on the HIV-1 integrase inhibitor 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)propenone (5CITEP). J Mol Struct 844–845:208–214. doi:10.1016/j.molstruc.2007.06.026
7 Density Functional Theory Calculations of Enzyme–Inhibitor …
86. Świderek K, Martí S., Moliner V (2012) Theoretical studies of HIV-1 reverse transcriptase
inhibition. Phys Chem Chem Phys 14(36):12614–12624. doi:10.1039/c2cp40953d
87. Liang YH, Chen FE (2007) ONIOM DFT/PM3 calculations on the interaction between dapivirine and HIV-1 reverse transcriptase, a theoretical study. Drug Discov Ther 1(1):57–60.
88. Garrec J, Sautet P, Fleurat-Lessard P (2011) Understanding the HIV-1 protease reactivity
with DFT: what do we gain from recent functionals?. J Phys Chem B 115(26):8545–8558.
doi:10.1021/jp200565w
89. Garrec J, Cascella M, Rothlisberger U, Fleurat-Lessard P (2010) Low inhibiting power of
N … CO based peptidomimetic compounds against HIV-1 protease: insights from a QM/
MM study. J Chem Theor Comput 6(4):1369–1379. doi:10.1021/ct9004728
90. Gautier A, Pitrat D, Hasserodt J (2006) An unusual functional group interaction and its potential to reproduce steric and electrostatic features of the transition states of peptidolysis.
Bioorg Med Chem 14(11):3835–3847. doi:10.1016/j.bmc.2006.01.031
91. Waibel M, Hasserodt J (2008) Diversity-oriented synthesis of a drug-like system displaying the distinctive N → C=O interaction. J Org Chem 73(16):6119–6126. doi:10.1021/
jo800719j
92 Waibel M, Pitrat D, Hasserodt J (2009) On the inhibition of HIV-1 protease by hydrazino-ureas displaying the N → C=O interaction. Bioorg Med Chem 17(10):3671–3679.
doi:10.1016/j.bmc.2009.03.059
93. Park C, Koh JS, Son YC, Choi H, Lee CS, Choy N, Moon KY, Jung WH, Kim SC, Yoon
H (1995) Rational design of irreversible, pseudo-C2-symmetric hiv-1 protease inhibitors.
Bioorg Med Chem Lett 5(16):1843–1848. doi:10.1016/0960-894X(95)00306-E
94. Lee CS, Choy N, Park C, Choi H, Son YC, Kim S, Ok JH, Yoon H, Kim SC (1996) Design,
synthesis, and characterization of dipeptide isostere containing cis-epoxide for the irreversible inactivation of HIV protease. Bioorg Med Chem Lett 6(6):589–594. doi:10.1016/0960894X(96)00087-X
95. Choy N, Choi H, Jung WH, Kim CR, Yoon H, Kim SC, Lee TG, Koh JS (1997) Synthesis
of irreversible HIV-1 protease inhibitors containing sulfonamide and sulfone as amide bond
isosteres. Bioorg Med Chem Lett 7(20):2635–2638. doi:10.1016/S0960-894X(97)10054-3
96. Kóňa J (2008) Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease. Org Biomol Chem 6(2):359–365.
doi:10.1039/b715828a
97. Pommier Y, Johnson AA, Marchand C (2005) Integrase inhibitors to treat HIV/AIDS. Nat
Rev Drug Discov 4(3):236–248. doi:10.1038/nrd1660
98. Ingale KB, Bhatia MS (2011) HIV-1 integrase inhibitors: a review of their chemical development. Antivir Chem Chemoth 22(3):95–105. doi:10.3851/IMP1740
99. Messiaen P, Wensing AMJ, Fun A, Nijhuis M, Brusselaers N, Vandekerckhove L (2013)
Clinical use of HIV integrase inhibitors: a systematic review and meta-analysis. PloS One
8(1):e52562. doi:10.1371/journal.pone.0052562
100. Liao C, Nicklaus MC (2010) Tautomerism and magnesium chelation of HIV-1 integrase inhibitors: a theoretical study. Chem Med Chem 5(7):1053–1066. doi:10.1002/
cmdc.201000039
101. Agrawal A, DeSoto J, Fullagar JL, Maddali K, Rostami S, Richman DD, Pommier Y, Cohen SM (2012) Probing chelation motifs in HIV integrase inhibitors. Proc Nat Acad Sci
U S A 109(7):2251–2256. doi:10.1073/pnas.1112389109
102. Thalheim T, Vollmer A, Ebert R-U, Kühne R, Schüürmann G (2010) Tautomer identification and tautomer structure generation based on the InChI code. J Chem Inf Model
50(7):1223–1232. doi:10.1021/ci1001179
103. Nunthaboot N, Pianwanit S, Parasuk V, Kokpol S, Wolschann P (2007) Theoretical study
on the HIV-1 integrase inhibitor 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)propenone (5CITEP). J Mol Struct 844–845:208–214. doi:10.1016/j.molstruc.2007.06.026
7 Density Functional Theory Calculations of Enzyme–Inhibitor …