F. F. Ammar, S. Abdel-azeim, L. Zargarian, Z. Hobaika, R. G. Maroun et al., Unprocessed viral DNA could be the primary target of the HIV-1 integrase inhibitor raltegravir, PLOS ONE, vol.7, issue.7, 2012.

F. F. Ammar, Z. Hobaika, S. Abdel-azeim, L. Zargarian, R. G. Maroun et al., A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity, FEBS Open Bio, vol.6, issue.4, 2016.

K. Anstett, B. Brenner, T. Mesplede, and M. A. Wainberg, HIV drug resistance against strand transfer integrase inhibitors, Retrovirology, vol.14, issue.1, 2017.

K. E. Hightower, R. Wang, F. Deanda, B. A. Johns, K. Weaver et al., Dolutegravir (S/GSK1349572) exhibits significantly slower dissociation than Raltegravir and Elvitegravir from wild type and integrase inhibitor-resistant HIV-1 integrase-DNA complexes, Antimicrobial Agents and Chemotherapy, vol.55, issue.10, 2011.

J. J. Hill and C. A. Royer, Fluorescence approaches to study of protein-nucleic acid complexation, Methods in Enzymology, vol.278, 1997.

Z. Hobaika, L. Zargarian, Y. Boulard, R. G. Maroun, O. Mauffret et al., Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase a4 helix, Nucleic Acids Research, vol.37, issue.22, 2009.

Z. Hobaika, L. Zargarian, R. G. Maroun, O. Mauffret, T. R. Burke et al., HIV-1 integrase and virus and cell DNAs: complex formation and perturbation by inhibitors of integration, Neurochemical Research, vol.35, issue.6, 2010.

P. R. Horn, Y. Mao, and M. Head-gordon, Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals, Physical Chemistry Chemical Physics, vol.18, issue.33, 2016.

M. A. Ibrahim, Molecular mechanical study of halogen bonding in drug discovery, Journal of Computational Chemistry, vol.32, issue.12, 2011.

T. Ikeda, H. Nishitsuji, X. Zhou, N. Nara, T. Ohashi et al., Evaluation of the functional involvement of human immunodeficiency virus type 1 integrase in nuclear import of viral cDNA during acute infection, Journal of Virology, vol.78, issue.21, 2004.

W. L. Jorgensen and P. Schyman, Treatment of halogen bonding in the OPLS-AA force field: application to potent anti-HIV agents, Journal of Chemical Theory and Computation, vol.8, issue.10, 2012.

R. Z. Khaliullin, E. A. Cobar, R. C. Lochan, A. T. Bell, and M. Head-gordon, Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals, Journal of Physical Chemistry A, vol.111, issue.36, 2007.

K. K. Koelsch and D. A. Cooper, Integrase inhibitors in salvage therapy regimens for HIV-1 infection, Current Opinion in HIV and AIDS, vol.4, issue.6, 2009.

M. Kolar and P. Hobza, On extension of the current biomolecular empirical force field for the description of halogen bonds, Journal of Chemical Theory and Computation, vol.8, 2012.

K. Kwapien, D. Damergi, S. Nader, E. Khoury, L. Hobaika et al., , 2017.

E. Khoury, PeerJ Physical Chemistry, 2019.

, Zn-binding group of metallo-?-lactamase inhibitors. Validation of a polarizable MM/MD potential by quantum chemistry, Journal of Physical Chemistry B, vol.121, issue.26

R. L. Lafemina, P. L. Callahan, and M. G. Cordingley, Substrate specificity of recombinant human immunodeficiency virus integrase protein, Virology, vol.65, issue.10, pp.5624-5630, 1991.

L. Lagardère, L. Jolly, F. Lipparini, F. Aviat, B. Stamm et al., Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields, Chemical Science, vol.9, issue.4, 2018.

P. Lesbats, A. N. Engelman, and P. Cherepanov, Retroviral DNA integration, Chemical Reviews, vol.116, issue.20, 2016.

X. Li, L. Krishnan, P. Cherepanov, and A. Engelman, Structural biology of retroviral DNA integration, Virology, vol.411, issue.2, 2011.

N. Mardirossian and M. Head-gordon, ?B97X-V: a 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy, Physical Chemistry Chemical Physics, vol.16, issue.21, 2014.

J. Marinello, C. Marchand, B. T. Mott, A. Bain, C. J. Thomas et al., Comparison of raltegravir and elvitegravir on HIV-1 integrase catalytic reactions and on a series of drug-resistant integrase mutants, Biochemistry, vol.47, issue.36, 2008.

M. Métifiot, C. Marchand, K. Maddali, and Y. Pommier, Resistance to integrase inhibitors, Viruses, vol.2, issue.7, pp.1347-1366, 2010.

M. Métifiot, C. Marchand, and Y. Pommier, HIV integrase inhibitors: 20-year landmark and challenges, Advances in Pharmacology, vol.67, 2013.

L. K. Naeger, P. Harrington, T. Komatsu, and D. Deming, Effect of dolutegravir functional monotherapy on HIV-1 virological response in integrase strand transfer inhibitor resistant patients, Antiviral Therapy, vol.21, issue.6, 2016.

D. A. Osterholzer and M. Goldman, Dolutegravir: a next-generation integrase inhibitor for treatment of HIV infection, Clinical Infectious Diseases, vol.59, issue.2, 2014.

J. P. Piquemal, N. Gresh, and C. Giessner-prettre, Improved formulas for the calculation of the electrostatic contribution to the intermolecular interaction energy from multipolar expansion of the electronic distribution, Journal of Physical Chemistry A, vol.107, issue.48, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02126882

P. Politzer, J. S. Murray, and C. T. , Halogen bonding: an electrostatically-driven highly directional noncovalent interaction, Physical Chemistry Chemical Physics, vol.12, issue.28, 2010.

Y. Pommier, A. A. Johnson, and C. Marchand, Integrase inhibitors to treat HIV/AIDS, Nature Reviews Drug Discovery, vol.4, issue.3, pp.236-248, 2005.

S. Y. Rhee, J. Taylor, W. J. Fessel, D. Kaufman, W. Towner et al., HIV-1 protease mutations and protease inhibitor cross-resistance, Antimicrobial Agents and Chemotherapy, vol.54, issue.10, 2010.

M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Gordon et al., , 1993.

E. Khoury, PeerJ Physical Chemistry, 2019.

, General atomic and molecular electronic structure system, Journal of Computational Chemistry, vol.14, issue.11

Y. Shao, Z. Gan, E. Epifanovsky, T. Gilbert, M. Wormit et al., Molecular Physics, vol.113, issue.2, pp.184-215

P. A. Sherman, M. L. Dickson, and J. A. Fyfe, Human immunodeficiency virus type 1 integration protein: DNA sequence requirements for cleaving and joining reactions, Virology, vol.66, issue.6, pp.3593-3601, 1992.

S. Simon, M. Duran, and J. J. Dannenberg, How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers, Journal of Chemical Physics, vol.105, issue.24, 1996.

A. J. Stone, Distributed multipole analysis, or how to describe a molecular charge distribution, Chemical Physics Letters, vol.83, issue.2, 1981.

A. J. Stone and M. Alderton, Distributed multipole analysis: methods and applications, Molecular Physics, vol.56, issue.5, 1985.

C. Tantillo, J. Ding, A. Jacobo-molina, R. G. Nanni, P. L. Boyer et al., Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase: implications for mechanisms of drug inhibition and resistance, Journal of Molecular Biology, vol.243, issue.3, 1994.

L. Vandekerckhove, GSK-1349572, a novel integrase inhibitor for the treatment of HIV infection, Current Opinion in Investigational Drugs, vol.11, issue.2, pp.203-212, 2010.

F. Vigné-maeder and P. Claverie, The exact multicenter multipolar part of a molecular charge distribution and its simplified representations, Journal of Chemical Physics, vol.88, issue.8, 1988.

E. Khoury, PeerJ Physical Chemistry, 2019.

M. A. Wainberg and Y. S. Han, Will drug resistance against dolutegravir in initial therapy ever occur?, Frontiers in Pharmacology, vol.6, 2015.

L. Wittkop, D. Breilh, D. Silva, D. Duffau, P. et al., Virological and immunological response in HIV-1-infected patients with multiple treatment failures receiving raltegravir and optimized background therapy, ANRS CO3 Aquitaine Cohort, Journal of Antimicrobial Chemotherapy, vol.63, issue.6, pp.1251-1255, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00372614

L. Zargarian, M. S. Benleumi, J. G. Renisio, H. Merad, R. G. Maroun et al., Strategy to discriminate between high and low affinity bindings of human immunodeficiency virus, type 1 integrase to viral DNA, Journal of Biological Chemistry, vol.278, issue.22, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00284918

X. Z. Zhao, S. J. Smith, D. P. Maskell, M. Métifiot, V. E. Pye et al., Structure-guided optimization of HIV integrase strand transfer inhibitors, Journal of Medicinal Chemistry, vol.60, issue.17, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02340319