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- Title
Design of a Novel and Selective IRAK4 Inhibitor Using Topological Water Network Analysis and Molecular Modeling Approaches.
- Authors
Lee, Myeong Hwi; Balupuri, Anand; Jung, Ye-rim; Choi, Sungwook; Lee, Areum; Cho, Young Sik; Kang, Nam Sook
- Abstract
Protein kinases are deeply involved in immune-related diseases and various cancers. They are a potential target for structure-based drug discovery, since the general structure and characteristics of kinase domains are relatively well-known. However, the ATP binding sites in protein kinases, which serve as target sites, are highly conserved, and thus it is difficult to develop selective kinase inhibitors. To resolve this problem, we performed molecular dynamics simulations on 26 kinases in the aqueous solution, and analyzed topological water networks (TWNs) in their ATP binding sites. Repositioning of a known kinase inhibitor in the ATP binding sites of kinases that exhibited a TWN similar to interleukin-1 receptor-associated kinase 4 (IRAK4) allowed us to identify a hit molecule. Another hit molecule was obtained from a commercial chemical library using pharmacophore-based virtual screening and molecular docking approaches. Pharmacophoric features of the hit molecules were hybridized to design a novel compound that inhibited IRAK4 at low nanomolar levels in the in vitro assay.
- Subjects
PROTEIN kinases; TARGETED drug delivery; CANCER treatment; STRUCTURE-activity relationship in pharmacology; MOLECULAR docking; MOLECULAR dynamics
- Publication
Molecules, 2018, Vol 23, Issue 12, p3136
- ISSN
1420-3049
- Publication type
Article
- DOI
10.3390/molecules23123136