John J. Barker

The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding.

Serine racemase is responsible for the synthesis of d-serine, an endogenous co-agonist for N-methyl-d-aspartate receptor-type glutamate receptors (NMDARs). This pyridoxal 5′-phosphate-dependent enzyme is involved both in the reversible conversion of l- to d-serine and serine catabolism by α,β-elimination of water, thereby regulating d-serine levels. Because d-serine affects NMDAR signaling throughout the brain, serine racemase is a promising target for the treatment of disorders related to NMDAR dysfunction. To provide a molecular basis for rational drug design the x-ray crystal structures of human and rat serine racemase were determined at 1.5- and 2.1-Å resolution, respectively, and in the presence and absence of the orthosteric inhibitor malonate. The structures revealed a fold typical of β-family pyridoxal 5′-phosphate enzymes, with both a large domain and a flexible small domain associated into a symmetric dimer, and indicated a ligand-induced rearrangement of the small domain that organizes the active site for specific turnover of the substrate.

Fragment-based identification of Hsp90 inhibitors.

Heat shock protein 90 (Hsp90) plays a key role in stress response and protection of the cell against the effects of mutation. Herein we report the identification of an Hsp90 inhibitor identified by fragment screening using a high‐concentration biochemical assay, as well as its optimisation by in silico searching coupled with a structure‐based drug design (SBDD) approach.

Binding Mode and Structure-Activity Relationships around Direct Inhibitors of the Nrf2-Keap1 Complex.

An X‐ray crystal structure of Kelch‐like ECH‐associated protein (Keap1) co‐crystallised with (1S,2R)‐2‐[(1S)‐1‐[(1,3‐dioxo‐2,3‐dihydro‐1H‐isoindol‐2‐yl)methyl]‐1,2,3,4‐tetrahydroisoquinolin‐2‐carbonyl]cyclohexane‐1‐carboxylic acid (compound (S,R,S)‐1 a) was obtained. This X‐ray crystal structure provides breakthrough experimental evidence for the true binding mode of the hit compound (S,R,S)‐1 a, as the ligand orientation was found to differ from that of the initial docking model, which was available at the start of the project. Crystallographic elucidation of this binding mode helped to focus and drive the drug design process more effectively and efficiently.

The multiple roles of computational chemistry in fragment-based drug design

Fragment-based drug discovery (FBDD) represents a change in strategy from the screening of molecules with higher molecular weights and physical properties more akin to fully drug-like compounds, to the screening of smaller, less complex molecules. This is because it has been recognised that fragment hit molecules can be efficiently grown and optimised into leads, particularly after the binding mode to the target protein has been first determined by 3D structural elucidation, e.g. by NMR or X-ray crystallography. Several studies have shown that medicinal chemistry optimisation of an already drug-like hit or lead compound can result in a final compound with too high molecular weight and lipophilicity. The evolution of a lower molecular weight fragment hit therefore represents an attractive alternative approach to optimisation as it allows better control of compound properties. Computational chemistry can play an important role both prior to a fragment screen, in producing a target focussed fragment library, and post-screening in the evolution of a drug-like molecule from a fragment hit, both with and without the available fragment-target co-complex structure. We will review many of the current developments in the area and illustrate with some recent examples from successful FBDD discovery projects that we have conducted.

Compound Design by Fragment-Linking

The linking together of two fragment compounds that bind to distinct protein sub‐sites can lead to a superadditivity of binding affinities, in which the binding free energy of the linked fragments exceeds the simple sum of the binding energies of individual fragments (linking coefficient E<1). However, a review of the literature shows that such events are relatively rare and, in the majority of the cases, linking coefficients are far from optimal being much greater than 1. It is critical to design a linker that does not disturb the original binding poses of each fragment in order to achieve successful linking. However, such an ideal linker is often difficult to design and even more difficult to actually synthesize. We suggest that the chance of achieving successful fragment linking can be significantly improved by choosing a fragment pair that consists of one fragment that binds by strong H‐bonds (or non‐classical equivalents) and a second fragment that is more tolerant of changes in binding mode (hydrophobic or vdW binders). We also propose that the fragment molecular orbital (FMO) calculations can be used to analyse the nature of the binding interactions of the fragment hits for the selection of fragments for evolution, merging and linking in order to optimize the chance of success.

Discovery and Structure–Activity Relationship of Potent and Selective Covalent Inhibitors of Transglutaminase 2 for Huntington’s Disease

Tissue transglutaminase 2 (TG2) is a multifunctional protein primarily known for its calcium-dependent enzymatic protein cross-linking activity via isopeptide bond formation between glutamine and lysine residues. TG2 overexpression and activity have been found to be associated with Huntingtons disease (HD); specifically, TG2 is up-regulated in the brains of HD patients and in animal models of the disease. Interestingly, genetic deletion of TG2 in two different HD mouse models, R6/1 and R6/2, results in improved phenotypes including a reduction in neuronal death and prolonged survival. Starting with phenylacrylamide screening hit 7d, we describe the SAR of this series leading to potent and selective TG2 inhibitors. The suitability of the compounds as in vitro tools to elucidate the biology of TG2 was demonstrated through mode of inhibition studies, characterization of druglike properties, and inhibition profiles in a cell lysate assay.

Inhibitors of phosphopantetheine adenylyltransferase.

Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in Coenzyme A biosynthesis. Because bacterial PPAT and mammalian PPAT are dissimilar, this enzyme is an attractive antibacterial target. Based on the structure of the substrate, 4-phosphopantetheine, a dipeptide library was designed, synthesised and tested against Escherichia coli PPAT. The most potent inhibitor PTX040334 was co-crystallised with E. coli PPAT. With this structural information, a rational iterative medicinal chemistry program was initiated, aimed at increasing the number of inhibitor-enzyme interactions. A very potent and specific inhibitor, PTX042695, with an IC(50) of 6 nM against E.coli PPAT, but with no activity against porcine PPAT, was obtained.

Fragment-Based Discovery of BACE1 Inhibitors Using Functional Assays

Novel nonpeptidic inhibitors of beta-secretase (BACE1) have been discovered by employing a fragment-based biochemical screening approach. A diverse library of 20000 low-molecular weight compounds were screened and yielded 26 novel hits that were confirmed by biochemical and surface plasmon resonance secondary assays. We describe here fragment inhibitors cocrystallized with BACE1 in a flap open and flap closed conformation as determined by X-ray crystallography.

Discovery of a Novel Hsp90 Inhibitor by Fragment Linking

Over the past decade, fragment screening has become an increasingly popular method for hit identification in drug discovery. Many methods can be successfully employed to identify fragment hits, however confirmation of a fragment hit and detailed analysis of the binding pose to its target is usually achieved by X-ray crystallographic analysis of the fragment protein complex. Subsequent optimisation involves the evolution of fragments to fully exploit binding pockets of a target or, where the chemistry of combining fragments is tractable, by the linking of fragments. Previously, we reported results from a fragment evolution process based on heat shock protein 90 (Hsp90) fragment hits; in the present report, we describe a fragment-linking approach that resulted in the rapid improvement in the level of Hsp90 inhibition. Hsp90 is a molecular chaperone with ATPase activity involved in the stabilisation of numerous client proteins including those involved in oncogenic transformations, such as BRaf. As such there continues to be considerable interest in the discovery of Hsp90 inhibitors. Previously, we reported the analysis of multiple crystal structures of diverse fragment complexes of Hsp90 derived from the primary fragment screen that demonstrated the flexibility of Hsp90 in the region of the adenosine binding site (see Figure 1). In particular, Hsp90 was found to adopt a helical conformation in the region of Asn 105 to Ile 110 in the presence of a subset of the fragments, including compound 2. The Hsp90–2 complex structure is essentially the same as the “closed” conformation previously reported for Hsp90 in the presence of geldanamycin. The helical conformation of Hsp90 creates a compact and well-defined pocket adjacent to the adenosine binding site. Other fragments, such as fragment 1, exclusively bind to the adenosine pocket and do not trigger the opening of the helical pocket. Both fragments 1 and 2 displayed relatively low inhibitory potencies against Hsp90 (IC50 = 1500 mm

Fragment-based discovery and optimization of BACE1 inhibitors.

A novel series of 2-aminobenzimidazole inhibitors of BACE1 has been discovered using fragment-based drug discovery (FBDD) techniques. The rapid optimization of these inhibitors using structure-guided medicinal chemistry is discussed.