Fragment-Based e-Pharmacophore Drug Screening. Tarek Kanan, Duaa Kanan, Ismail Erol, Serdar Durdagi. Faculty of Medicine, Department of Computational ...
Identifying Novel Inhibitors of NF-kB/IkBα Complex via Fragment-Based e-Pharmacophore Drug Screening Tarek Kanan, Duaa Kanan, Ismail Erol, Serdar Durdagi
Faculty of Medicine, Department of Computational Medicinal Chemistry and Biophysics, Bahcesehir University, Istanbul, Turkey
INTRODUCTION • NF-kB (nuclear factor kappa B) is a master regulator of the body’s innate and adaptive immunity. • It represents a conserved family of transcription factors in eukaryotes. • NF-κB is found in the cytoplasm bound to IκBa proteins. • The pathway can be activated by certain stimuli including proinflammatory cytokines, TNF (tumor necrosis factor) or PAMPS (pathogen-associated molecular patterns) such as lipopolysaccharides in gram negative bacteria. • Signals lead to phosphorylation of IkBα, targeting it for degradation by the ubiquitin-proteasome pathway. • Consequently, NF-kB is free to translocate to the nucleus and bind DNA to enhance gene expression. • NF-kB is upregulated in certain cancers such as diffuse B cell lymphoma, chronic inflammation, autoimmune diseases as well as heart disease and neurodegenerative diseases. • Corticosteroids are able to mediate their antiinflammatory effect by increasing IkBα thus inhibiting NFkB translocation to the nucleus. • A variety of antioxidants such as vitamin E derivates can also inhibit NF-kB activation.
METHODS
RESULTS & DISCUSSION
• Here, we present an in-silico study to investigate the p50/p65 (RelA) heterodimer complex of NF-kB in association with its inhibitor IkBα, and aim to find potent inhibitors with strong binding affinities via fragment-based virtual e-pharmacophore screening, followed by docking of the top compounds, and molecular simulation and energy analyses.
• Our study presents the first e-pharmacophore model of the NF-kB/IkBα complex.
Identification of the binding site from literature and confirmation using SiteMap®
Receptor cavity e-pharmacophore generation using Glide XP scores Pharmacophore screening of OTAVAchemicals compound collection (~260,000)
• Fitness and docking scores were compared with known NF-kB inhibitors. • Novel compounds were found with better docking and fitness scores than known inhibitors from the literature.
Figure 2. The 5-sited receptor cavity e-pharmacophore model of the NF-kB (p50/p65)/IkBα complex via the projected points donor methodology. The top XP-docked 85,000 fragments from ZINC Clean Fragments Library (~2 million) and Schrodinger’s Glide Fragment Library (~670) were used to generate the epharmacophore hypothesis (AANRR). A = H-bond acceptor; D= H-bond donor; R= aromatic ring; N= negative ionizable group.
Docking of the top 1000 screened ligands
RelA (p65)
Analysis of the resulting docking and fitness scores
Therapeutic & toxicity profile analyses
Figure 1. A ribbon representation of the NF-kB/IkBα complex and their binding site which was used for molecular docking and e-pharmacophore hypothesis generation. IkBα (barrel-like shaped protein on left) is in contact with the NF-kB complex formed by the p50 (blue)-RelA/p65 (yellow) heterodimer. The binding site is made up majorly of ligand acceptor (red) and ligand donor (blue) maps as well as few hydrophobic maps (yellow). This binding site was computationally generated by SiteMap, and supported by literature findings.
• Six e-pharmacophore hypotheses were generated.
Docking of ZINC Clean Fragments Library (~2 million) and Schrodinger’s Glide Fragment Library (~670)
IkBα
p50
• Our hypotheses are built based on 85,000 fragments (the highest number available in literature).
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Figure 3. Fitness and XP docking scores of known NF-kB inhibitors (left) and compounds from the OTAVAchemicals library collection (right) after screening by the 5-sited e-pharmacophore projected point model. 84 known NF-kB inhibitors were screened, but only 6 compounds successfully met the minimum requirement of matching at least 4 featured ligand sites. About 260,000 compounds from the OTAVAchemicals library collection were also screened, and the top 1000 screened compounds were retained and are plotted.
CONCLUSIONS • Getting insight into the complexity of NF-kB signalling pathways requires an integration of the hundreds of biochemical, molecular and computational studies conducted so far since its discovery 30 years ago. • Finding potent inhibitors that could act more selectively at the NF-kB/IkBα complex may present a novel therapy for cancer as well as other inflammatory conditions, and lead the way to future drug design efforts and experimental studies.
