Miles Stuart Congreve

Crystal structure of human soluble adenylate cyclase reveals a distinct, highly flexible allosteric bicarbonate binding pocket.

Soluble adenylate cyclases catalyse the synthesis of the second messenger cAMP through the cyclisation of ATP and are the only known enzymes to be directly activated by bicarbonate. Here, we report the first crystal structure of the human enzyme that reveals a pseudosymmetrical arrangement of two catalytic domains to produce a single competent active site and a novel discrete bicarbonate binding pocket. Crystal structures of the apo protein, the protein in complex with α,β‐methylene adenosine 5′‐triphosphate (AMPCPP) and calcium, with the allosteric activator bicarbonate, and also with a number of inhibitors identified using fragment screening, all show a flexible active site that undergoes significant conformational changes on binding of ligands. The resulting nanomolar‐potent inhibitors that were developed bind at both the substrate binding pocket and the allosteric site, and can be used as chemical probes to further elucidate the function of this protein.

Chapter 28 Fragment-Based Lead Discovery

Publisher Summary Fragment-based lead discovery (FBLD) is establishing itself as an approach that holds the promise of delivering leads with greater efficiency and speed when compared to high throughput screening (HTS). In FBLD, small libraries of low molecular weight compounds (typically 120–250 Da) are screened using sensitive biophysical techniques to detect weak binding. Lower absolute affinity of fragments is expected compared to much higher molecular weight hits detected by HTS due to their reduced size and complexity. Through the use of structural biology, it is often then relatively straightforward to optimize these hits to promising lead molecules. There have been a number of recent reviews on fragment-based methods of which two reviews are important that were published in 2004. The reviews aimed at medicinal chemists and gave comprehensive lists of examples of how lead molecules have been derived starting from fragments. This chapter focuses on examples that have been published since these two reviews and, where the starting fragment is less than 300 Da and has an affinity against the target of 425 mM. The latter criterion means that it would have been difficult to identify the hits using conventional screening methods. The chapter provides an overview of binding mode of the fragments underlining the view that efficient optimization of fragments requires a structure-based approach. The chapter briefly outlines the identification of fragments where the optimization is either not described, or only a limited amount of optimization was achieved. Examples are given where lead molecules were successfully derived from fragments.

Abstract A211: Fragment‐based drug discovery of the synthetic small molecule HSP90 inhibitor AT13387

Heat Shock Protein 90 (HSP90) is a member of a family of molecular chaperone proteins which directs the folding of polypeptides into functional configurations affecting stabilisation and activation. Many of these proteins are oncogenes regulating tumor cell growth, survival and apoptosis. This poster will focus on the screening and medicinal chemistry work that led to the identification of AT13387, a high affinity HSP90 inhibitor that is currently in clinical trials for the treatment of cancer. A fragment screening campaign was conducted against the N‐terminal domain of HSP90 to detect very low molecular weight compounds (Molecular Weight Subsequent lead optimisation focussed on the improvement of in vivo distribution properties via the addition of basic moieties to the lead molecule. These compounds showed encouraging in vivo pharmacology and biological profiles, and further medicinal chemistry work led to the discovery of AT13387, an inhibitor with sub‐nanomolar affinity, prolonged duration of action and excellent in vivo anti‐tumor efficacy. This poster represents first disclosure of the structure of AT13387 and illustrates how a fragment‐based drug discovery approach can be efficiently used to discover compounds suitable for clinical testing in oncology. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):A211.