Structure Activity Relationship by NMR and by Computer:  A Comparative Study

Abstract

There has recently been considerable interest in using NMR spectroscopy to identify ligand binding sites of macromolecules. In particular, a modular approach has been put forward by Fesik et al. (Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Science 1996, 274, 1531-1534) in which small ligands that bind to a particular target are identified in a first round of screening and subsequently linked together to form ligands of higher affinity. Similar strategies have also been proposed for in silico drug design, where the binding sites of small chemical groups are identified, and complete ligands are subsequently assembled from different groups that have favorable interactions with the macromolecular target. In this paper, we compare experimental and computational results on a selected target (FKBP12). The binding sites of three small ligands ((2S)1-acetylprolinemethylester, 1-formylpiperidine, 1-piperidinecarboxamide) in FKBP12 were identified independently by NMR and by computational methods. The subsequent comparison of the experimental and computational data showed that the computational method identified and ranked favorably ligand positions that satisfy the experimental NOE constraints.

Force field parameters for the simulation of modified histone tails

“…The united-atom parameters for small functional groups representing methylated lysine were tested on multiple target proteins for which structural information is available. With post-processing of the MCSS calculations by a continuum solvent approach, 27, 28 excellent agreement with experimental structures is obtained.…”

“…29 Following the determination of the minima for each group, a post-processing step that consists of calculating an approximate relative free energy of binding that includes effects of solvation was done following the method presented earlier. 27,32 The specific parameters used in the post-processing were γ = 5kcal/mol/Å 2 for the surface term and ε = 80 and 4 for the water and protein interior, respectively. Clustering of the post-processed functional group minima was done based on the van der Waals contacts made by that functional group with the protein residues.…”

“…Clustering of the post-processed functional group minima was done based on the van der Waals contacts made by that functional group with the protein residues. 27 For each minimum, a list of all protein residues that have a significant van der Waals interaction with the functional group is produced. We refer to this list as the van der Waals signature, which can be used for comparison purposes.…”

“…This allowed us to test whether the parameters would correctly predict a high affinity binding site for the modified histone tail residue at the experimentally determined position. The post-processing procedure has been independently validated in previous studies 27,32 and shown to make reliable prediction when a correct force field is available. When apo structures of the histone binding partner were available, the MCSS procedure was repeated using the apo structure to see if a high affinity binding site could still be identified at the experimental position, even in the presence of small distortions of the binding site as could be found in apo structures.…”

“…This evaluation was performed using the MCSS docking procedure with post-processing to account for solvent effect 27 (see Material and Methods) to identify the binding pocket. The predictive ability of the docking protocol has been established previously on ligands for which a validated force field was available.…”