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Molecular insight into the interaction mechanisms of an annulated pyrazole (DB08446) with HIV-1 RT: a QM and QM/QM' study

  1. Author:
    Wang, Yueping
    Wang, Jiangyuan
    Zhong, Peng
    Li, Yiming
    Lai, Christopher
    He, Yanping

  2. Author Address

    Kunming Univ Sci & Technol, Dept Appl Chem, Fac Sci, Kunming 650500, Yunnan, Peoples R China.Yunnan Univ, Sch Chem Sci & Technol, Key Lab Med Chem Nat Resource, Minist Educ, Kunming 650091, Yunnan, Peoples R China.NCI, Biol Chem Lab, Ctr Canc Res, Frederick, MD 21702 USA.
    1. Year: 2018
    2. Date: Oct
  2. Journal: MONATSHEFTE FUR CHEMIE
  3. SPRINGER WIEN,
    1. 149
    2. 10
    3. Pages: 1919-1929
  5. Type of Article: Article
  6. ISSN: 0026-9247
  1. Abstract:

    Quantum mechanical and hybrid QM/QM' ONIOM methodology have been applied to investigate the structure and molecular interactions between DB08446 and the binding site of HIV-1 RT. The binding energy calculated using the ONIOM2(M06-2X-D3/6-311 + G(2df,2p):PM6) method is - 369.43 kJ/mol, demonstrating that DB08446 can strongly bind to HIV-1 RT. The pairwise interaction energy analysis at the M06-2X-D3/6-311 + G(2df,2p) and RI-PWPB95-D3/def2-QZVPP levels of theory disclose that there are more attractive interactions than repulsive interactions in the binding site. In particular, residues Lys103, Va1106, Tyr188, and Trp229 were major contributors for DB08446 binding to HIV-1 RT. Further detailed structure analysis and NCI visualization confirm that the H-bond, X-bond, pi-pi, CH center dot center dot center dot pi, and van der Waals interactions, etc. were the dominant stabilization factors of non -bonded interaction between DB08446 and the binding site of HIV-1 RT.

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External Sources

  1. View Full Text
  2. DOI: 10.1007/s00706-018-2239-2
  3. View record in Web of Science®
  4. WOS: 000448664600021

Library Notes

  1. Fiscal Year: FY2018-2019
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