Ronald Knegtel

Discovery of potent and selective inhibitors of ataxia telangiectasia mutated and Rad3 related (ATR) protein kinase as potential anticancer agents.

DNA-damaging agents are among the most frequently used anticancer drugs. However, they provide only modest benefit in most cancers. This may be attributed to a genome maintenance network, the DNA damage response (DDR), that recognizes and repairs damaged DNA. ATR is a major regulator of the DDR and an attractive anticancer target. Herein, we describe the discovery of a series of aminopyrazines with potent and selective ATR inhibition. Compound 45 inhibits ATR with a K(i) of 6 nM, shows >600-fold selectivity over related kinases ATM or DNA-PK, and blocks ATR signaling in cells with an IC(50) of 0.42 μM. Using this compound, we show that ATR inhibition markedly enhances death induced by DNA-damaging agents in certain cancers but not normal cells. This differential response between cancer and normal cells highlights the great potential for ATR inhibition as a novel mechanism to dramatically increase the efficacy of many established drugs and ionizing radiation.

The discovery of the potent aurora inhibitor MK-0457 (VX-680).

The identification of a novel series of Aurora kinase inhibitors and exploitation of their SAR is described. Replacement of the initial quinazoline core with a pyrimidine scaffold and modification of substituents led to a series of very potent inhibitors of cellular proliferation. MK-0457 (VX-680) has been assessed in Phase II clinical trials in patients with treatment-refractory chronic myelogenous leukemia (CML) or Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ALL) containing the T315I mutation.

EFFICACY AND SELECTIVITY IN FLEXIBLE DATABASE DOCKING

Flexible database docking with DOCK 4.0 has been evaluated for its ability to retrieve biologically active molecules from a database of approximately 1,000 compounds with known activities against thrombin and the progesterone receptor. The retrieval of known actives and chemically similar but inactive molecules was monitored as a function of conformational and orientational sampling. The largest enrichment of actives among the 10% highest ranking molecules is obtained when only five conformations are used to seed the next round of ligand reconstruction and limited sampling is applied to place the base fragment in the binding site. The performance of energy and chemical scoring, as implemented in DOCK 4.0, was found to depend on the protein used for docking. For the progesterone receptor, energy scoring yields the largest enrichments (64%) in terms of actives retrieved among the 10% top scoring molecules, while chemical scoring performs best for thrombin (94%). With the exception of the application of energy scoring to the progesterone receptor, both energy‐based scoring schemes applied in this study do not discriminate well between true actives and chemically similar but inactive compounds. In conclusion, flexible docking is able to effectively prioritize high‐throughput screening databases, using less conformational sampling than normally required for appropriate reconstruction of protein‐ligand complexes. The more subtle discrimination between chemically similar classes of active and inactive compounds remains, however, problematic. Proteins 1999:37:334–345. ©1999 Wiley‐Liss, Inc.

Discovery and structure-activity relationship of 3-aminopyrid-2-ones as potent and selective interleukin-2 inducible T-cell kinase (Itk) inhibitors

Interleukin-2 inducible T-cell kinase (Itk) plays a role in T-cell functions, and its inhibition potentially represents an attractive intervention point to treat autoimmune and allergic diseases. Herein we describe the discovery of a series of potent and selective novel inhibitors of Itk. These inhibitors were identified by structure-based design, starting from a fragment generated de novo, the 3-aminopyrid-2-one motif. Functionalization of the 3-amino group enabled rapid enhancement of the inhibitory activity against Itk, while introduction of a substituted heteroaromatic ring in position 5 of the pyridone fragment was key to achieving optimal selectivity over related kinases. A careful analysis of the hydration patterns in the kinase active site was necessary to fully explain the observed selectivity profile. The best molecule prepared in this optimization campaign, 7v, inhibits Itk with a K(i) of 7 nM and has a good selectivity profile across kinases.

Comparison of the Accuracy of Experimental and Predicted pKa Values of Basic and Acidic Compounds

PurposeAssessment of the accuracy of experimental and theoretical methods of pKa determination for acids and bases as separate classes.MethodsFour literature pKa datasets were checked for errors and pKa values assigned unambiguously to a single acidic and/or basic ionisation centre. A new chemically diverse and drug-like dataset was compiled from high-throughput UV–vis spectrophotometry pKa data. Measured pKa values were compared with data obtained by alternative methods and predictions by the Epik, Chemaxon and ACD pKa DB software packages.ResultsThe pKa values of bases were considerably less accurately predicted than those of acids, in particular for structurally complex bases. Several new chemical motifs were identified for which pKa values were particularly poorly predicted. Comparison of pKa values obtained by UV–vis spectrophotometry and different literature sources revealed that low aqueous solubility and chromophore strength can affect the accuracy of experimental pKa determination for certain bases but not acids.ConclusionsThe pKa prediction tools Epik, Chemaxon and ACD pKa DB provide significantly less accurate predictions for bases compared to acids. Certain chemical features are underrepresented in currently available pKa data sets and as a result poorly predicted. Acids and bases need to be considered as separate classes during pKa predictor development and validation.

A method to identify and screen libraries of guests that complex to a synthetic host

Molecular docking with a large number of guests, followed by experimental verification, was used to determine the selectivity of a synthetic host molecule and resulted in a hit rate of 30 % (see schematic outline of procedure). The identification of ligands for a given receptor by means of screening may represent a paradigm shift in supramolecular host–guest chemistry.

Kinetic and mechanistic characterisation of Choline Kinase-α

Choline Kinase is a key component of the Kennedy pathway that converts choline into a number of structural and signalling lipids that are essential for cell growth and survival. One member of the family, Choline Kinase-α (ChoKα) is frequently up-regulated in human cancers, and expression of ChoKα is sufficient to transform cells. Consequently ChoKα has been studied as a potential target for therapeutic agents in cancer research. Despite great interest in the enzyme, mechanistic studies have not been reported. In this study, a combination of initial velocity and product inhibition studies, together with the kinetic and structural characterisation of a novel ChoKα inhibitor is used to support a mechanism of action for human ChoKα. Substrate and inhibition kinetics are consistent with an iso double displacement mechanism, in which the γ-phosphate from ATP is transferred to choline in two distinct steps via a phospho-enzyme intermediate. Co-crystal structures, and existing site-specific mutation studies, support an important role for Asp306, in stabilising the phospho-enzyme intermediate. The kinetics also indicate a distinct kinetic (isomerisation) step associated with product release, which may be attributed to a conformational change in the protein to disrupt an interaction between Asp306 and the phosphocholine product, facilitating product release. This study describes a mechanism for ChoKα that is unusual amongst kinases, and highlights the availability of different enzyme states that can be exploited for drug discovery.

A Role for Hydration in Interleukin-2 Inducible T Cell Kinase (Itk) Selectivity.

The selectivity profile of kinase inhibitors is commonly explained in terms of favourable or unfavourable interactions between the inhibitor and active site residues. In practice residue sequence differences have not always been sufficient to explain observed selectivity profiles. A series of interleukin‐2 inducible T cell kinase (Itk, EC 2.7.10.2) inhibitors that achieve selectivity through the introduction of a single nitrogen atom in an aromatic ring has recently been discovered. Structures of these inhibitors bound to Itk showed this nitrogen to be solvent exposed and not involved in any direct interactions with the enzyme. By analysing active site hydration, using the molecular dynamics tool WaterMap, the observed selectivity profile can be explained in terms of the replacement of a thermodynamically unfavourable water molecule by the inhibitor and improved hydration of the bound ligand. The location of this hydration site was successfully used to enrich virtual screening results in their content of selective Itk inhibitors.

Advances in the design of ITK inhibitors

Introduction: ITK is a member of the Tec family of nonreceptor protein tyrosine kinases that plays a central role in T-cell signaling. Its inhibition is seen as an attractive approach to the treatment of immune-mediated disorders. Insight into the function of ITK has emerged from studies on ITK-deficient mice, which exhibit defects in T-cell receptor (TCR) signaling and immune responses to pathogens. Although knockout studies provide an important contribution to the understanding of ITK inhibition, they have limitations in predicting the viability of small-molecule ITK inhibitors as therapeutic agents. Areas covered: Since the original publication of the structural information on the ITK enzyme, there have been a number of reports disclosing the discovery of ITK inhibitors from various chemical scaffolds. The authors present and describe the approaches followed by the various research groups in the field. An assessment of the various chemical tools available to the scientific community is also discussed, both from a biochemical and a structural point of view. Expert opinion: The majority of currently available ITK inhibitors either lack comprehensive selectivity data or evidence of their ability to effectively suppress T-cell signaling in cells or animal models. Although inhibitors targeting an inactive conformation of ITK have yielded the predicted phenotype, it remains unclear to what extent the observed biological activity is due to inhibition of the kinase activity of ITK. With available biological data suggesting the possibility of functional redundancy of ITK, the suitability of ITK as a potential molecular target for the development of new immunosuppressant drugs remains to be confirmed.

Structure-based optimization of aminopyridines as PKCθ inhibitors

The identification of a novel series of PKCθ inhibitors and subsequent optimization using docking based on a crystal structure of PKCθ is described. SAR was rapidly generated around an amino pyridine-ketone hit; (6-aminopyridin-2-yl)(2-aminopyridin-3-yl)methanone 2 leading to compound 21 which significantly inhibits production of IL-2 in a mouse SEB-IL2 model.