Abstract
WaterLOGSY is a sensitive ligand-observed NMR experiment for detection of interaction between a ligand and a protein and is now well-established as a screening technique for fragment-based lead discovery. Here we develop and assess a protocol to derive ligand epitope mapping from WaterLOGSY data and demonstrate its general applicability in studies of fragment-sized ligands binding to six different proteins (glycogen phosphorylase, protein peroxiredoxin 5, Bcl-xL, Mcl-1, HSP90, and human serum albumin). We compare the WaterLOGSY results to those obtained from the more widely used saturation transfer difference experiments and to the 3D structures of the complexes when available. In addition, we evaluate the impact of ligand labile protons on the WaterLOGSY data. Our results demonstrate that the WaterLOGSY experiment can be used as an additional confirmation of the binding mode of a ligand to a protein.
Highlights
Fragment-based lead discovery (FBLD)[1,2] is maturing as an effective method for generating small molecules that modulate the activity of biological molecules, usually proteins
The comparison of the two WaterLOGSY spectra is similar to the comparison of saturation-transfer difference (STD) and STDoff spectra, with the WaterLOGSY bound spectrum corresponding to the STD spectrum and the WaterLOGSY free spectrum corresponding to the STDoff spectrum[30]
Our results clearly demonstrate that the comparison of WaterLOGSY intensities for a small molecule in its free and protein-bound forms allows the identification of the ligand solventexposed protons
Summary
Fragment-based lead discovery (FBLD)[1,2] is maturing as an effective method for generating small molecules that modulate the activity of biological molecules, usually proteins. The central idea is to screen a small number (typically 1000 s) of low molecular weight (usually less than 250 Da) compounds against a protein target of interest, mostly using a sensitive biophysical technique that can detect binding with an affinity as weak as low mM (KD for dissociation)[2,3,4]. Hit fragments are optimised by either growing or merging features of compounds to generate lead molecules. Such molecules can subsequently be used as tools to probe the biology of a protein or be further optimised to give clinical candidates such as the recently approved medicines, vemurafenib, and venetoclax[5,6]. The assessment of the ligand binding mode is a critical information that provides important guidance for the identification of suitable modification locations in fragment optimisation
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Journal of Enzyme Inhibition and Medicinal Chemistry
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
