Corrigendum to “The Conformation and Orientation of a 27-Residue CCR5 Peptide in a Ternary Complex with HIV-1 gp120 and a CD4-Mimic Peptide” [J. Mol. Biol. 410/5 (2011) 778–797]

Schnur, Einat; Noah, Eran; Ayzenshtat, Inbal; Sargsyan, Hasmik; Inui, Tatsuya; Ding, Fa‐Xiang; Arshava, Boris; Sagi, Yoav; Kessler, Naama; Levy, Rina; Scherf, Tali; Naider, Fred; Anglister, Jacob

doi:10.1016/j.jmb.2012.02.029

Cited by 1 publication

(1 citation statement)

References 1 publication

(1 reference statement)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The crystal structure 4MBS also has missing amino‐(N) terminal domain which is necessary for HIV entry. Hence, we retrieved N terminal residues 7–27 of CCR5 from PDB server (PDB ID, 2L87) [35] ; the two fragments were combined using pairwise alignment on their overlapping regions. The remaining missing part of N terminal residues 1–7 were modeled using crosslink proteins tool and the loop refinement tool of Prime module [36] .…”

Section: Methodsmentioning

confidence: 99%

Drug Re‐positioning Studies for Novel HIV‐1 Inhibitors Using Binary QSAR Models and Multi‐target‐drivenIn SilicoStudies

Doğan

Durdağı

2020

Molecular Informatics

View full text Add to dashboard Cite

Current antiretroviral therapies against HIV involve the usage of at least two drugs that target different stages of HIV life cycle. However, potential drug interactions and side effects pose a problem. A promising concept for complex disease treatment is ‘one molecule‐multiple target’ approach to overcome undesired effects of multiple drugs. Additionally, it is beneficial to consider drug re‐purposing due to the cost of taking a drug into the market. Taking these into account, here potential anti‐HIV compounds are suggested by virtually screening small approved drug molecules and clinical candidates. Initially, binary QSAR models are used to predict the therapeutic activity of around 7900 compounds against HIV and to predict the toxicity of molecules with high therapeutic activities. Selected compounds are considered for molecular docking studies against two targets, HIV‐1 protease enzyme, and chemokine co‐receptor CCR5. The top docking poses for all 549 molecules are then subjected to short (1 ns) individual molecular dynamics (MD) simulations and they are ranked based on their calculated relative binding free energies. Finally, 25 molecules are selected for long (200 ns) MD simulations, and 5 molecules are suggested as promising multi‐target HIV agents. The results of this study may open new avenues for the designing of new dual HIV‐1 inhibitor scaffolds.

show abstract

Section: Methodsmentioning

confidence: 99%