Docking and molecular dynamics calculations of some previously studied and newly designed ligands to catalytic core domain of HIV-1 integrase and an investigation to effects of conformational changes of protein on docking results
Yükleniyor...
Dosyalar
Tarih
2017-01-09
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Türkiye Kimya Derneği
Erişim Hakkı
info:eu-repo/semantics/openAccess
Attribution-NonCommercial-ShareAlike 3.0 United States
Attribution-NonCommercial-ShareAlike 3.0 United States
Özet
Nowadays, AIDS still remains as a worldwide pandemic and continues to cause
many deaths which arise from HIV-1 virus. For nearly 35 years, drugs that target various
steps of virus life cycle have been developed. HIV-1 integrase constitutes one of these
steps which is essential for virus life cycle. Computer-aided drug design is being used in
many drug development and drug improvement studies as also used in development of
the first HIV-1 integrase inhibitor Raltegravir. In this study, 3 ligands which are already
used as HIV-1 integrase inhibitors and 4 newly designed ligands were docked to catalytic
core domain of HIV-1 integrase. Each ligand docked to three different conformations of
protein. Prepared complexes (21 items) were carried out by 50 ns MD simulations and
results were analyzed. Finally, the binding free energies of ligands were calculated. It was
determined that designed ligands L01 and L03 gave favorable results. The questions about
the ligands which have low docking scores in a conformation of protein could give better
scores in another conformation of protein and if the MD simulations carry the different
oriented and different localized ligands in same position at the end of simulation were
answered.
Açıklama
Anahtar Kelimeler
HIV-1 Integrase, Drug Design, Docking, Molecular Dynamics, Binding Free Energy
Kaynak
WoS Q Değeri
N/A
Scopus Q Değeri
Q4
Cilt
4
Sayı
1
Künye
Ercan, S. (2017). Docking and molecular dynamics calculations of some previously studied and newly designed ligands to catalytic core domain of HIV-1 integrase and an investigation to effects of conformational changes of protein on docking results. Journal of the Turkish Chemical Society, Section A: Chemistry, 4 (1), pp. 243-270. https://doi.org/10.18596/jotcsa.287327
