Poster Presentation The 44th Lorne Conference on Protein Structure and Function 2019

Rapid Elaboration of Fragments into Leads (REFiL). A systematic approach to fragment elaboration. (#162)

Menachem J Gunzburg 1 , Luke A Adams 1 , Bradley C Doak 1 , Stephen J Headey 1 , Craig Morton 2 , Jamie Simpson 3 , Martin J Scanlon 1 3
  1. Monash Fragment Based Drug Design Platform, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
  2. Biochemistry and Molecular Biology, Bio21 Institute, Parkville, Victoria, Australia
  3. Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia

Fragment Based Drug Design (FBDD) is a method of finding lead compounds by searching for small chemical fragments which may bind weakly but efficiently, and elaborating them to generate leads with high affinity. One of the major hurdles in FBDD is developing the initial low affinity fragment hits found through various screening methods into higher affinity lead like structures and beyond.1 This is particularly difficult without the aid of structural data, hence we have developed a strategy for the Rapid Elaboration of Fragments into Leads (REFiL).

We have constructed a library of ~1200 fragments for primary screening with the aim of balancing physicochemical properties, dissimilarity, chemical space coverage, synthetic tractability and suitability for our fragment development process. Each fragment has at least 20 commercially available analogues, which enables us to validate, prioritise and rank fragment hits, facilitates rapid analogue screening and allows early SAR to be generated. Our library is an evolution of a previous library used for NMR-based fragment screening against numerous targets. All fragments used for screening have purity >90%, confirmed solubility at 1 mM in aqueous buffer, are not prone to aggregation and show little to no binding at SPR reference surfaces.

Our new workflow for fragment hit development utilises the strategy of off-rate screening (ORS) that was developed by Vernalis.2 We have used chemoinformatics to design reactive reagent libraries suitable for high throughput and parallel small scale synthesis that explore diverse chemical space, and support all of the most commonly reported medicinal chemistry transformations . At its heart, REFiL uses ORS by Surface Plasmon Resonance (SPR) on minimally purified compounds to prioritise elaborated fragments for synthesis and characterisation and can be applied without knowledge of the target protein structure.

Here we demonstrate the use and validation of REFiL to elaborate fragment hit compounds rapidly allowing >20-fold improvement in KD by using off-rate screening of designed diverse elaborated fragment libraries.

  1. Hann & Keserü Nat. Rev. Drug Discov. 2012, 11(5), 355-365
  2. Murray, et. al. J. Med. Chem. 2014, 57(7), 2845–2850.