• 10.1073/pnas.97.17.9367
  • Proceedings of the National Academy of Sciences
  • Volume 97
  • August 2000
  • pp 9367-9372

Site-directed ligand discovery

Important contribution to fragment hit-finding technologies


Topic Area
Biology / biological chemistry
Article Type
Primary Research

Logic / Design


Point of Paper
Very clear
Experimental Design
Excellent
Main Conclusions
Supported by evidence presented

Reproducibility


Key Procedures
Able to reproduce most
# Procedures Attempted
1 to 3
Of Attempted, # Reproduced
All

Improvements


Replicated Methods Exactly:
Major Changes
Reviewer Improvements
Slight improvements

Versatility


Applicability to Other Fields
Definitely
Use in Own Work
Yes, and it was useful

Clarity


Overall Clarity
Very good

Impact


Impact
Signifcantly advances the field

Transparency


Funding Sources
Clearly disclosed
Conflicts of Interest
Yes
Conflict Disclosure
Clearly disclosed

Other


Safety Concerns
None or clearly mentioned

Details


This paper by Erlanson and colleagues describes the disulfide tethering technique, which has proven to be a reproducible and versatile method for finding fragment hits. The main advance is the covalent targeting of the fragment library to a specific site on a protein surface. They convincingly show the mechanism and effectiveness of this approach with crystal structures of hits bound to E. Coli  Thymidylate Synthase.

I used a similar disulfide fragment library to perform screens on a variety of protein targets during the late 2010s. The method for that work is published in https://doi.org/10.1177/2472555217732072, but there are a few key advancements that have been made Erlanson's seminal paper. Firstly, we now use much smaller amounts of protein (femtomoles, or 1-5 uL injections of single-digit nM concentrations). This allows much faster Liquid Chromatography step, and since the library size is small (~1500 compounds), we removed the pooling of compounds to allow for higher quality mass spectrometry (MS) data. This allowed us to process the entire library in 1-2 days, and collect data with high enough qualitu to build a automated analysis pipeline.

Importantly, the core method described in Erlanson's paper was not modified. We screened dozens and dozens of proteins and were able to reliably identify fragment binders. The major hiccups when applying disulfide tethering to a new target are 1) the ability of the protein sample to fly in an established intact protein LCMS method and 2) the number and reacitivity of surface-exposued cysteines on the target. Some protein engineering (point mutations to remove non-target cysteines) may be necessary, and a robust way to purify the target protein is important, since the assay mixture is injected directly on to the LCMS.



Leave a Comment