Divide-and-conquer-based quantum chemical study for interaction between HIV-1 reverse transcriptase and MK-4965 inhibitor

Patchreenart Saparpakorn, Masato Kobayashi, Supa Hannongbua, Hiromi Nakai

    Research output: Contribution to journalArticle

    5 Citations (Scopus)

    Abstract

    MK-4965, 3-{5-[(6-Amino-1H-pyrazolo[3,4-b]pyridine-3-yl)methoxy]-2- chlorophenoxy}-5-chloro-benzonitrile, is a novel non-nucleoside reverse transcriptase inhibitor (NNRTI) revealing high levels of potency against wild-type (WT) the human immunodeficiency virus type-1 (HIV-1) and some important mutants. The divide-and-conquer (DC) based Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory (MP2) calculations were performed for the binding modes of MK-4965 in the reverse transcriptase (RT) of the WT HIV-1 and a mutant Y181C, 181 tyrosine mutated by cysteine. The binding pockets of MK-4965 consisting of 19 residues are selected for the study. Numerical assessments confirmed the efficiency and accuracy of the DC-MP2 method in comparison with the conventional MP2 one. Subsystem interaction energies obtained by the DC-MP2 calculations clarified the key parts of the binding between MK-4965 and HIV-1: hydrogen bonding with 102 lysine, which is apart from mutated 181 residue. The present information can give a helpful guide for the future inhibitor design.

    Original languageEnglish
    Pages (from-to)510-517
    Number of pages8
    JournalInternational Journal of Quantum Chemistry
    Volume113
    Issue number4
    DOIs
    Publication statusPublished - 2013 Feb 15

    Fingerprint

    human immunodeficiency virus
    inhibitors
    Viruses
    lysine
    tyrosine
    cysteine
    interactions
    Reverse Transcriptase Inhibitors
    RNA-Directed DNA Polymerase
    pyridines
    perturbation theory
    Lysine
    Cysteine
    Tyrosine
    Hydrogen bonds
    hydrogen
    Human immunodeficiency virus 1 reverse transcriptase
    3-(5-((6-amino-1H-pyrazolo(3,4-b)pyridine-3-yl)methoxy)-2-chlorophenoxy)-5-chlorobenzonitrile
    energy

    Keywords

    • DC-MP2
    • HIV-1 RT
    • interaction energy
    • MK-4965
    • Mulliken charge

    ASJC Scopus subject areas

    • Condensed Matter Physics
    • Atomic and Molecular Physics, and Optics
    • Physical and Theoretical Chemistry

    Cite this

    Divide-and-conquer-based quantum chemical study for interaction between HIV-1 reverse transcriptase and MK-4965 inhibitor. / Saparpakorn, Patchreenart; Kobayashi, Masato; Hannongbua, Supa; Nakai, Hiromi.

    In: International Journal of Quantum Chemistry, Vol. 113, No. 4, 15.02.2013, p. 510-517.

    Research output: Contribution to journalArticle

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