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Fragment-Based Approaches in Drug Discovery and Chemical Biology Duncan E. Scott, Anthony G. Coyne, Sean A. Hudson, and Chris Abell*
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Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom ABSTRACT: Fragment-based approaches to finding novel small molecules that bind to proteins are now firmly established in drug discovery and chemical biology. Initially developed primarily in a few centers in the biotech and pharma industry, this methodology has now been adopted widely in both the pharmaceutical industry and academia. After the initial success with kinase targets, the versatility of this approach has now expanded to a broad range of different protein classes. Herein we describe recent fragment-based approaches to a wide range of target types, including Hsp90, β-secretase, and allosteric sites in human immunodeficiency virus protease and fanesyl pyrophosphate synthase. The role of fragment-based approaches in an academic research environment is also examined with an emphasis on neglected diseases such as tuberculosis. The development of a fragment library, the fragment screening process, and the subsequent fragment hit elaboration will be discussed using examples from the literature.
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iterative small-to-large-molecule chemistry strategy means that lead development is guided by combining structural and assay information generated at each step in the program. There is now a growing body of published work to support the power of this approach. An important landmark was passed in 2011 when Zelboraf (PLX4032) became the first FDA-approved drug developed using the fragment-based approach.1,2 Despite this, there is still more progress that needs to be made in the implementation of this approach. The origins of FBDD can be traced to a seminal paper published by Jencks in which it is proposed that small “fragments”, although weakly binding, form high-quality interactions that can be optimized into highly potent larger molecules.3 Another notable contribution to the early thinking in this field came from Verlinde who developed a method to link together low-molecular mass fragments to develop more potent compounds against trypanosomiasis.4 The methodology became established though the pioneering studies at Abbott using SAR by NMR5 and Astex,6,7 where the use of X-ray crystallography was, and still is, the main screening platform. FBDD was initially successful when it was employed principally against kinase targets that proved to be highly druggable and well-suited to the approach. Subsequently, it has become clear that the approach is generic and can be applied successfully to any protein family for which structural information is readily available, and indeed, there are examples of success with fragment-based methods against targets that have proven to be very difficult with traditional HTS approaches.8,9 Fragmentbased methods are now being used against targets as diverse as
he discovery of new molecules for modulating biological function is a key motivation in chemical biology and the primary focus in drug discovery programs. Over the past two decades, the pharmaceutical industry has become very reliant on high-throughput screening (HTS) approaches, to screen large libraries of compounds (up to 106), that they have assimilated over time. Maintaining the diversity and quality of these libraries is a major overhead and requires constant attention. Inevitably, the libraries contain molecules that are not very druglike; i.e., they are relatively lipophilic and have poor thermodynamic solubility. As a consequence, false positives arise, and even genuine hits may not be good starting points for drug development. It is also inevitable that these HTS libraries represent only a very tiny fraction of possible chemical space and so limit confidence in finding a really good starting point for subsequent development. Finally, even if the structure of a HTS hit binding to the target protein can be obtained, it may still not be clear which parts of the molecule contribute most to the binding energy, leading to ambiguity about how best to increase potency. Fragment-based methods, which involve the elaboration of weakly binding small molecules with molecular masses of
