Targeting the NF-κB/IκBα complex via fragment-based E-Pharmacophore virtual screening and binary QSAR models

Abstract

Nuclear factor-κB (NF κB) transcription factors represent a conserved family of proteins that regulate not only immune cells, but also heart cells, glial cells and neurons, playing a fundamental role in various cellular processes. Due to its dysregulation in certain cancer types as well as in chronic inflammation and autoimmune diseases, it has recently been appreciated as an important therapeutic target. The aim of this study was to investigate the binding pocket of NF κB (p50/p65) heterodimer complex in association with NF κB inhibitor IκBα to identify potent ligands via fragment-based e-pharmacophore screening. The ZINC Clean Fragments (~2 million) and the Schrodinger's medically relevant Glide fragments library (~670) were used to create the e-pharmacophore models at the potential binding site of the target which was validated by site mapping. Glide/HTVS docking was conducted followed by re-docking of the top 20% fragments by Glide/SP and Glide/XP protocols. The top-85000 Glide XP-docked fragments were used to generate the e-pharmacophore hypotheses. The Otava small molecule library (~260000 drug-like molecules) and additional 85 known NF κB inhibitors were screened against the derived e-pharmacophore models. The top-1000 high-scored molecules, which were well aligned to the e-pharmacophore models, from the Otava small molecule library, were then docked into the binding pocket. Finally, the selected 88 hit molecules and the 85 known inhibitors were analyzed by the MetaCore/MetaDrug™ platform, which uses developed binary QSAR models for therapeutic activity prediction as well as pharmacokinetic and toxicity profile predictions of screening molecules. Ligand selection criteria led to the refinement of 3 potent hit molecules using molecular dynamics (MD) simulations to better investigate their structural and dynamical profiles. The selected hit molecules had a low toxicity and a significant therapeutic potential for heart failure, antiviral activity, asthma and depression, all conditions in which NF κB plays a critical role. These hit ligands were also structurally stable at the NF-κB/IκBα complex as per the MD simulations and MM/GBSA analysis. Two of these ligands (Otava IDs: 1426436 and 6248112) were energetically more favorable and therefore are hypothesized to be more potent. Identifying new potent NF κB/IκBα inhibitors may thus present a novel therapy for inflammation-mediated conditions as well as cancer, facilitating more efficient research, and leading the way to future drug development efforts.

Post-translational Modifications of IκBα: The State of the Art

“…Moreover, a new method, fragment-based virtual E-pharmacophore screening, has been developed to promote the development of drug design targeting on the NF-κB/IκBα complex (Kanan et al, 2019). An excellent study conducted by Kanan et al investigated the structure of the binding pocket of NF-κB p65/p50 heterodimer complex with IκBα in detail, and therefore constructed the e-pharmacophore models to discover potential ligands with strong binding affinity as candidate NF-κB/IκBα inhibitors.…”

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

“…We have therefore performed root mean square deviations (RMSD) calculations throughout the MD simulations, especially for C α atoms of protein structures. Additionally, we have checked the RMSD of the ligand molecules by considering two different fitting modes: ‘fit on protein/profit’ and ‘fit on ligand/ligfit’ [58] . While the first fitting mode indicates the structural stability of ligand with respect to protein i. e. its translational motion, the second mode shows the internal fluctuations of the ligand atoms in its binding pocket i. e. its rotational motion.…”

Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2

“…Estimated QSAR values (normalized between 0 and 1) >0.5 indicate potential therapeutic activity. The details about QSAR models could be found in the following reference (Kanan et al, 2019). In the current study, we used "cancer-QSAR" model, which has the following parameters: Training set N = 886, Test set N = 167, Sensitivity = 0.89, Specificity = 0.83, Accuracy = 0.86, MCC = 0.72.…”

“…Different strategies depending on the availability of target molecules have been developed; structure-based drug design in which the target structure is known and ligand-based drug design that could be applied in cases that target structure is not known. It is also possible to combine both approaches to increase the possibility of "hit molecule" discovery as has been done in our previous studies (Durdagi et al, 2018a,b;Zaka et al, 2018;Kanan et al, 2019;Mollica et al, 2019). The most widely used technique in target-driven-based drug design is the molecular docking, and there are various docking programs as well as many different scoring functions to rank binding poses.…”