Abstract SY05-01: Fragment-based drug discovery: Less is more
Authors: Heightman Tom D. 
Published: May 2015

Over the past decade, fragment-based drug discovery (FBDD) has become increasingly widely used across industry and academia, as highlighted recently (1). This is likely driven by the successful identification of leads for targets considered intractable using conventional screening strategies, in addition to delivering leads with improved physicochemical properties for more tractable targets such as kinases (2).

The fundamental concept of fragment screening is to use simpler molecules so that the chemical space can be sampled much more efficiently than is possible when using molecules of greater complexity (3). One consequence of screening smaller, simpler fragments is that their affinity is expected to be relatively low (&gt;1 mM), given the limited numbers of potential interactions that they can make with the protein, and the detection of low-potency fragment hits presents substantial technical challenges. However, although weak in potency, fragment hits make high-quality interactions with the protein as they must overcome a substantial entropic barrier to binding, relative to their size, and their binding thereby frequently occurs with high efficiencies.

We now have experience of over 30 high-throughput crystallographic and biophysical fragment screens against a broad range of protein classes, and our results support the view that less complex molecules give a higher hit rate. This rich dataset of protein-fragment interactions has allowed continuous optimization of our fragment library, to maximize both success in fragment screening campaigns, and synthetic efficiency during fragment development. In addition, the ability to routinely produce multiple iterations of fast-turnaround crystallography has proven invaluable in guiding medicinal chemistry optimization, allowing parsimonious building of affinity, which provides drug candidates with enhanced ligand efficiency likely to minimize attrition in development.

The success of the approach will be illustrated by the fragment-based discovery of novel dual inhibitors of protein-protein interactions involving XIAP and cIAP1.

XIAP and cIAP1 are members of the inhibitor of apoptosis protein (IAP) family, a class of proteins that can down-regulate the apoptosis process by inhibiting caspases and other apoptotic factors (4). A defining feature of these proteins is the presence of three Baculoviral IAP Repeat (BIR) domains in their sequence. SMAC (second mitochondrial activator of caspases) is released by mitochondria in response to apoptotic stimuli and deactivates the function of IAPs through binding of its N-terminal region (AVPI) to the IAP-BIR domains. This event disrupts protein-protein interactions between IAPs and caspases and promotes apoptosis. It has recently been demonstrated that dual antagonism of both XIAP and cIAP1 is required to achieve a strong apoptotic response (5).

Several companies and academic groups have active programs developing SMAC peptidomimetic compounds for the treatment of cancer. These compounds are based on the key alanine motif in AVPI which engenders cIAP1 selectivity (IC50 values for AVPI vs XIAP-BIR3 and cIAP1-BIR3 are 0.3 uM and 0.016 uM respectively).

Our fragment-based screening approach, PyramidTM, enabled us to identify a non-alanine fragment which binds with similar affinity for both XIAP and cIAP1. Hit optimisation using a structure-based approach led to the discovery of a dual XIAP and cIAP1 antagonist with potent in vivo pharmacodynamic activity when delivered orally in a mouse xenograft model. High concentrations of the compound were measured in tumor and plasma over a 24 h period which ensured potent antagonism of both XIAP and cIAP1. Induction of apoptosis biomarkers (cleaved PARP, cleaved caspase-3) and strong inhibition of tumor growth were also observed for this new class of inhibitors.

References

1. M. Baker, Nature Rev. Drug Discov. 2013, 12, 5.

2. P. Leeson & S. St-Gallay, Nature Reviews Drug Discovery 2011, 10, 749.

3. M.M. Hann, A.R. Leach & G. Harper, J. Chem. Inf. Comput. Sci. 2001, 41, 856.

4. S. Fulda & D. Vucic, Nat. Rev. Drug Disc. 2012, 11, 109.

5. C. Ndubaku et al, ACS Chem. Biol. 2009, 4, 557.

Citation Format: Tom D. Heightman. Fragment-based drug discovery: Less is more. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY05-01. doi:10.1158/1538-7445.AM2014-SY05-01