Ligand deconstruction: Why some fragment binding positions are conserved and others are not

Abstract

Fragment-based drug discovery (FBDD) relies on the premise that the fragment binding mode will be conserved on subsequent expansion to a larger ligand. However, no general condition has been established to explain when fragment binding modes will be conserved. We show that a remarkably simple condition can be developed in terms of how fragments coincide with binding energy hot spots—regions of the protein where interactions with a ligand contribute substantial binding free energy—the locations of which can easily be determined computationally. Because a substantial fraction of the free energy of ligand binding comes from interacting with the residues in the energetically most important hot spot, a ligand moiety that sufficiently overlaps with this region will retain its location even when other parts of the ligand are removed. This hypothesis is supported by eight case studies. The condition helps identify whether a protein is suitable for FBDD, predicts the size of fragments required for screening, and determines whether a fragment hit can be extended into a higher affinity ligand. Our results show that ligand binding sites can usefully be thought of in terms of an anchor site, which is the top-ranked hot spot and dominates the free energy of binding, surrounded by a number of weaker satellite sites that confer improved affinity and selectivity for a particular ligand and that it is the intrinsic binding potential of the protein surface that determines whether it can serve as a robust binding site for a suitably optimized ligand.

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery

“…In agreement with the key role of this hot spot, it was shown that a fragment hit retains its binding mode if it overlaps with a large enough fraction of CC1, and thus can efficiently exploit the potential interaction energy that this site provides [51]. If the fragment binds to a location outside CC1, or within CC1 but without achieving sufficiently high overlap, there is no guarantee that it will remain at that position upon expansion of the fragment into a larger ligand.…”

“…Whether a bound fragment will have a robust binding mode also depends largely on CC1. Specifically, a fragment hit will retain its binding mode if it binds at CC1, provided it overlaps well enough with CC1 to efficiently exploit the potential of this site to generate noncovalent interaction energy [51]. In contrast, if a fragment binds at a site other than CC1, there is no guarantee that it will remain at that position upon further elaboration.…”

“…FO is defined by FO = N F /N T , where N T denotes the total number of non-hydrogen atoms of all probe molecules in CC1, and N F is the number of such atoms that are within 2 Å from any non-hydrogen atom of the fragment in its bound position. Thus, FO measures the fraction of CC1 occupied by the fragment, weighted according to the energetic importance of each region within the hot spot as measured by the local density of probe atoms [51]. It was shown that if a fragment binds at the primary hot spot, has fractional overlap over 0.8, and has acceptable ligand efficiency (LE >0.3) [40], then its binding mode is very likely conserved upon extension.…”

Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia

“…56 Babaoglu and Shoichet deconstructed a -lactamase inhibitor into fragments with 8, 11 and 14 heavy atoms and observed that the fragments did not preserve the binding mode corresponding to the same moiety in the full inhibitor. 57 Satoh et al 58 examples that fragments bound with appropriate overlap with the hot spot of consensus clusters preserve their binding mode, 65 while those bound at the site of other clusters may change their binding mode upon structure expansion. It is also consistent with the fact that although fragments are versatile binders with the ability to bind to various protein targets, they can also be evolved to higher specificity for the more druggable targets.…”

“…65 They suggest that secondary binding sites tend to have less potential to conserve binding modes for fragments and their larger derivatives.…”