How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study Using N-Myristoyltransferases as a Model System

Abstract

A model system of two related enzymes with conserved binding sites, namely N-myristoyltransferase from two different organisms, was studied to decipher the driving forces that lead to selective inhibition in such cases. Using a combination of computational and experimental tools, two different selectivity-determining features were identified. For some ligands, a change in side chain flexibility appears to be responsible for selective inhibition. Remarkably, this was observed for residues orienting their side chains away from the ligands. For other ligands, selectivity is caused by interfering with a water molecule that binds stronger to the off-target than to the target. Based on this finding, a virtual screen for selective compounds was conducted resulting in three hit compounds with the desired selectivity profile. This study delivers a guideline on how to assess selectivity-determining features in proteins with conserved binding sites and to translate this knowledge into the design of selective inhibitors.

QSAR and Pharmacophore Modeling of Nitrogen Heterocycles as Potent Human N-Myristoyltransferase (Hs-NMT) Inhibitors

“…The developed QSAR models have successfully satiated values for many fitting, cross-validation, and external validation parameters. A high value of R2tr, R2cv (Q2loo), Q2LMO, and CCCcv indicates the statistical robustness of the developed models [16,20,32,34,[37][38][39]. In addition, Y-scrambling results also confirm this observation.…”

“…This observation is also supported by the pharmacophore modeling and crystal structure of Hs-NMT-1 in complex with various ligands. Recently, Kersten et al [37] reported that sulphonamide derivatives bearing Nitrogen heterocycles interact with hydrophobic residue Tyr296 (pdb code 3IWE and 6FZ5), which vindicates the importance of the presence of hydrophobic atoms in the ligand.…”

“…A comparison of Figures 8 and 9 indicates that the consensus pharmacophore model and the pharmacophore model obtained using the x-ray resolved crystal structure of extracted ligands have good similarity with each other, especially with respect to the presence of the hydrophobic region (green colored) at the center and two H-bond acceptors (red colored). Thus, QSAR and pharmacophore modeling led to identification of consensus and complementary structural features and vindicated by recent crystal structures [37].…”

Protein-Based Virtual Screening Tools Applied for RNA–Ligand Docking Identify New Binders of the preQ1-Riboswitch

“…Finally, solvation and desolvation effects upon ligand binding and water-mediated interactions should be elucidated. While explicit solvation sites within protein binding pockets can have a huge impact on affinity and selectivity, , it is more than likely that similar effects account for RNA-binding sites as well. However, within the RNA–ligand docking test set presented, only 18 structures with a resolution below 2.0 Å allow sufficiently accurate determination of explicit water molecules.…”

Protein-based Virtual Screening Tools applied for RNA-Ligand Docking identify new Binders of the preQ1-Riboswitch

“…Lastly, solvation and desolvation effects upon ligand binding and water-mediated interactions should be elucidated. While explicit solvation sites within protein binding pockets can have an huge impact on affinity and selectivity, 113,114 it is more than likely that similar effects account for RNA binding sites as well. However, within the RNA-ligand docking test set presented, only 18 structures with a resolution below 2.0 Å allow sufficiently accurate determination of explicit water molecules.…”