Osamu Ichihara

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

BackgroundThe reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex molecular interactions. Full quantum mechanical (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment molecular orbital (FMO) method. This approximate molecular orbital method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estimation of ligand binding affinity. Additionally, the FMO method can be combined with approximations for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes.ResultsWe applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calculated the binding affinity for 28 CDK2 inhibitors using the abinitio FMO method based on a number of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calculated and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examined and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calculation allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calculation, the entropic component and solvation terms are neglected. For this reason a more accurate and predictive estimate for binding free energy was desired. Therefore, additional terms used to describe the protein-ligand interactions were then calculated to improve the correlation of the FMO derived values to experimental free energies of binding. These terms were used to account for the polar and non-polar solvation of the molecule estimated by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), respectively, as well as a correction term for ligand entropy. A quantitative structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) analysis of the ligand potencies and the calculated terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 molecule test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 molecules was well predicted (r2 = 0.842), and could be used to obtain meaningful estimations of the binding free energy.ConclusionsOur results show that binding energies calculated with the FMO method correlate well with published data. Analysis of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with additional terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the absolute values obtained by FMO alone.

GAMESS As a Free Quantum-Mechanical Platform for Drug Research

Driven by a steady improvement of computational hardware and significant progress in ab initio method development, quantum-mechanical approaches can now be applied to large biochemical systems and drug design. We review the methods implemented in GAMESS, which are suitable to calculate large biochemical systems. An emphasis is put on the fragment molecular orbital method (FMO) and quantum mechanics interfaced with molecular mechanics (QM/MM). The use of FMO in the protein-ligand binding, structure-activity relationship (SAR) studies, fragment- and structure-based drug design (FBDD/SBDD) is discussed in detail.

Fragment-based identification of Hsp90 inhibitors.

Heat shock proteinu200590 (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 inu2005silico searching coupled with a structure‐based drug design (SBDD) approach.

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.

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

Irreversible 4-Aminopiperidine Transglutaminase 2 Inhibitors for Huntington's Disease.

A new series of potent TG2 inhibitors are reported that employ a 4-aminopiperidine core bearing an acrylamide warhead. We establish the structure-activity relationship of this new series and report on the transglutaminase selectivity and in vitro ADME properties of selected compounds. We demonstrate that the compounds do not conjugate glutathione in an in vitro setting and have superior plasma stability over our previous series.

Novel MK2 inhibitors by fragment screening.

Inhibitors of MAPKAP kinase 2 (MK2) are expected to attenuate the p38alpha signal transduction pathway in macrophages in a similar way to p38alpha inhibitors and to have a lower propensity for toxic side effects that have slowed the clinical development of the latter. Therefore, novel MK2 inhibitors may find therapeutic application in acute and chronic, TNFalpha-mediated inflammatory conditions like rheumatoid arthritis and others. Herein we have applied fragment screening, using physiologically relevant bioassays and fragment binding mode mapping by protein-observed NMR spectroscopy to the discovery of novel efficient chemical starting points for MK2.

Development of Self-Indicating Resin

Previously, we have reported the development and application of self-indicating resins (SIR), materials which can indicate presence or absence of amines in the reaction solution by the conspicuous color change of a phenolsulfophthalein type dye immobilized on resin beads [2a]. Although the functionality necessary for attaching the dye to the resins could be readily introduced by the Suzuki-Miyaura coupling during the synthesis of the SIR 1, this approach was only applicable to the dyes containing suitable functionality for the cross-coupling reaction. In this article we describe a new approach of immobilizing the indicating dyes onto the resin support. The dyes suitable for loading onto aminomethyl polystyrene (PS) resin were prepared by Friedel-Crafts reaction of 2-sulfoterephthalic anhydride with a wide range of phenols. Using this new route, the SIR 6c was readily prepared in >100g quantities. Use of the SIR 6c in the synthesis of a 144 member urea library was demonstrated and the SIR successfully indicated the endpoint of the reaction between amines and isocyanates.