The effect of K-252a, a potent microbial inhibitor of protein kinase, on activated cyclic nucleotide phosphodiesterase

Identifying the proteins to which small-molecule probes and drugs bind in cells

Most small-molecule probes and drugs alter cell circuitry by interacting with 1 or more proteins. A complete understanding of the interacting proteins and their associated protein complexes, whether the compounds are discovered by cell-based phenotypic or target-based screens, is extremely rare. Such a capability is expected to be highly illuminating--providing strong clues to the mechanisms used by small-molecules to achieve their recognized actions and suggesting potential unrecognized actions. We describe a powerful method combining quantitative proteomics (SILAC) with affinity enrichment to provide unbiased, robust and comprehensive identification of the proteins that bind to small-molecule probes and drugs. The method is scalable and general, requiring little optimization across different compound classes, and has already had a transformative effect on our studies of small-molecule probes. Here, we describe in full detail the application of the method to identify targets of kinase inhibitors and immunophilin binders.

MIXED-LINEAGEKINASES: A Target for the Prevention of Neurodegeneration

The activation of the c-Jun N-terminal kinase (JNK) pathway is critical for naturally occurring neuronal cell death during development and may be important for the pathological neuronal cell death of neurodegenerative diseases. The small molecule inhibitor of the mixed-lineage kinase (MLK) family of kinases, CEP-1347, inhibits the activation of the JNK pathway and, consequently, the cell death in many cell culture and animal models of neuronal death. CEP-1347 has the ability not only to inhibit cell death but also to maintain the trophic status of neurons in culture. The possible importance of the JNK pathway in neurodegenerative diseases such as Alzheimer's and Parkinson's diseases provides a rationale for the use of CEP-1347 for the treatment of these diseases. CEP-1347 has the potential of not only retarding disease progression but also reversing the severity of symptoms by improving the function of surviving neurons.

A radioactive binding assay for inhibitors of trkA kinase

The high-affinity receptor for nerve growth factor (NGF), trkA, is a receptor-linked tyrosine kinase. The binding of NGF to trkA, depending on the context of its environment, can cause beneficial or deleterious responses in the target cells. For example, the activation of trkA in sympathetic and sensory neurons causes the subsequent survival and differentiation of these cells. On the other hand, the activation of trkA by NGF in other cells has been implicated in several pathologies including inflammation-induced hyperalgesia and several cancers. A radioactive binding assay to evaluate inhibitors of the kinase domain of trkA has been developed and validated. The assay monitors the specific binding of an inhibitor of trkA kinase activity, the indolocarbazole K-252a, to the trkA receptor. [3H]K-252a binds with high affinity to one site on the cytoplasmic kinase domain of the trkA receptor. Binding is saturable and reversible with a dissociation constant (Kd) of 1.5 nM. The binding assay has been used in competition binding experiments to determine the inhibition constants for other indolocarbazole compounds. The IC50 values for compounds obtained in the binding assay correlate very well with the IC50 values obtained in an enzyme-linked immunosorbent assay for trkA tyrosine kinase activity.

Induction of giant endothelial cells in culture by K-252a, a protein kinase inhibitor

K-252a, a protein kinase inhibitor with a wide spectrum of activity, inhibited the serum-stimulated proliferation of cultured bovine carotid endothelial cells dose-dependently, and all the cells became remarkably large, with a diameter of more than 150 microns at K-252a concentrations of 0.3-1 microgram/ml. This effect of the agent was reproducible under the conditions described in this article. When the endothelial cells became abnormally large by K-252a, the surface area of the cell became wider, and the F-actin molecules increased in both number and length. Despite their abnormal size, K-252a-induced giant cells maintained at least three physiological functions characteristic to normal endothelial cells: 1) ability to take up acetylated low density lipoprotein, 2) ability to produce and secrete endothelin and 3) ability to respond via an increase of [Ca2+]i to the stimulation by bradykinin. These observations suggest that K-252a-induced giant cells are useful tools for examining the function of endothelial cells because it is very reproducible and can be produced by an easy treatment.

Affinity labeling of bovine brain protein kinase C by tosyl lysyl chloromethane. A kinetic study

The kinetics of inactivation of bovine brain protein kinase C (PKC) by N alpha-p-tosyl L-lysyl chloromethane (TosLysCH2Cl) were investigated. In absence of activators PKC gave non-linear semilog inactivation plots. At each reagent concentration a plateau of residual activity was reached after some time; its value was inversely proportional to TosLysCH2Cl concentration but the plateau was not due to inactivator depletion. On the other hand, in the presence of Ca2+, phosphatidylserine and phorbol 12-myristate 13-acetate, the activity loss followed saturation kinetics, with k(inact) = 0.6 x 10(-3) s-1 and Kinact = 1.9 mM. The study of protection effects by ATP Mg2+ and histone required the presence of 50% glycerol in the incubation mixtures, otherwise the controls (kinase in the presence of activators and ATP Mg2+ or histone) rapidly lost activity. In the presence of 50% glycerol, the inactivation parameters were somewhat altered (k(inact) = 0.3 x 10(-3) s-1 and K(inact) = 0.2 mM); ATP Mg2+ proved to afford a mixed competitive-non competitive protection effect, while histone protected in a competitive manner with a Kp of 0.06 microgram/ml. In the presence and the absence of glycerol, plots of log k(obs) versus log inactivator concentration yielded straight lines with slopes of 0.7-0.9, indicating that 1 mol of reagent is sufficient for inactivation. The results described in this paper suggest that the reagent TosLysCH2Cl hits the catalytic domain of activated PKC at the active site, which is not available in resting PKC; in non-activated PKC, the labeling site would be different.

K-252 compounds: modulators of neurotrophin signal transduction

K-252 compounds, which share a common polyaromatic aglycon structure, are rather general and potent inhibitors of various protein kinases, including protein kinase C and tyrosine-specific protein kinases, and possibly act by interfering at or near the ATP binding site. However, chemical modifications in their sugar moiety can result in high specificity of the inhibitory action and, furthermore, can induce other stimulatory and inhibitory effects on nerve cells. These compounds are of particular interest because, in intact cells, they inhibit the actions of NGF and other neurotrophins without diminishing comparable actions of other growth factors. This effect seems to reflect a direct inhibitory action on trk neurotrophin receptor proteins. At concentrations lower than those necessary to inhibit neurotrophin actions, K-252a and K-252b have been shown to potentiate the stimulatory effects of NT-3 on different neurons in culture and on PC12 cells. The structural requirements for this effect seem to be different from those for the inhibition of neurotrophin actions. These findings raise the possibility of development of compounds of high selectivity, able to inhibit or potentiate the transduction mechanisms of individual neurotrophins, and identify K-252a and K-252b as lead compounds for the development of such selective molecules. Specific inhibitors and stimulators of neurotrophins would be valuable tools to investigate biological functions of the neurotrophins in vitro and in vivo. Furthermore, it is possible that, in the future, highly selective drugs with agonistic or antagonistic actions on neurotrophin mechanisms could become therapeutically useful in the treatment of neurological disease and injury.

Antitumor effect of KT6124, a novel derivative of protein kinase inhibitor K-252a, and its mechanism of action

Novel derivatives of K-252a, (8R*,9S*,11S*)-(-)-9-hydroxy-9-methoxycarbonyl- 8-methyl-2,3,9,10-tetrahydro-8,11-epoxy-1H,8H,11H-2,7b,11a-triazadibe nzo[a,g]-cycloocta[cde]trinden-1-one, an inhibitor of protein kinases and calmodulin-dependent phosphodiesterase, were synthesized and evaluated for their antitumor activity in vitro and in vivo. Of ten derivatives tested, four were active against the P388 murine leukemia i.p.-i.p. system, although K-252a was inactive. Among these derivatives, KT6124 was selected for further biological evaluation studies because its efficacy was the highest. KT6124 was also active against sarcoma 180 and B16 melanoma. It exerted a relatively broad spectrum of antiproliferative activity against 20 human tumor cell lines in vitro. To determine the mechanism(s) of action underlying the antitumor activity of KT6124, we tested the drug for inhibition of protein kinases, including Ca(2+)- and phospholipid-dependent protein kinase (PKC), in intact A431 human epidermoid carcinoma cells in comparison with the PKC-inhibitory activity of K-252a. KT6124 did not antagonize the action of phorbol 12-myristate 13-acetate (PMA) in A431 cells, whereas K-252a did, suggesting that KT6124 may not act on protein kinases in the cells. The interaction of KT6124 with DNA in living cells was examined by the alkaline elution method. KT6124 apparently exhibited DNA scission both dose- and time-dependently in the target cells. The DNA breakage was dependent on proteinase K treatment, suggesting its possible interaction with DNA-related enzyme(s). These results indicate that KT6124 exerts antitumor activity by acting on DNA or on DNA-related enzyme(s) in tumor cells rather than via the inhibition of protein kinases.

Inhibition of nerve growth factor-induced neurite outgrowth of PC12 cells by a protein kinase inhibitor which does not permeate the cell membrane

K-252a, a protein kinase inhibitor of microbial origin, has proven to be a specific inhibitor of nerve growth factor. In this study, the effects of K-252b, the 9-carboxylic acid derivative of K-252a, on nerve growth factor-induced neurite outgrowth in PC12 cells was examined. K-252b is hydrophilic and does not permeate the cell membrane of PC12 cells, whereas K-252a clearly does. K-252b is, however, as potent as K-252a itself in inhibiting the nerve growth factor-induced neurite outgrowth. These results can be interpreted to suggest that effects of K-252b may be through surface-bound/anchored K-252b-sensitive molecules on PC12 cells.

Effect of K252a, a protein kinase inhibitor, on the proliferation of vascular smooth muscle cells

In the growth arrested cultures of bovine carotid smooth muscle, K252a (10 - 100 ng/ml), a protein kinase inhibitor with wide spectrum suppressed the cell proliferation induced by TPA and increase of serum. K252a was more potent in the antiproliferative activity than H7, a C-kinase-specific inhibitor, but less than staurosporine, another wide-spectrum protein kinase inhibitor. Since C-kinase plays an important role in the signal transduction leading to the cell proliferation and K252a inhibits C-kinase in vitro, the antiproliferative effect of K252a to carotid smooth muscle cells is likely to be exerted through c-kinase dependent pathway.

Inhibition by new anthraquinone compounds, K-259-2 and KS-619-1, of calmodulin-dependent cyclic nucleotide phosphodiesterase

K-259-2 and KS-619-1, novel anionic anthraquinone metabolites isolated from culture broth of microorganisms, inhibited activation of bovine brain phosphodiesterase induced by calmodulin (CaM), sodium oleate, or limited proteolysis with almost equal potency. The inhibition of calmodulin-activated phosphodiesterase (CaM-PDE) by K-259-2 or KS-619-1 was overcome by a higher concentration of CaM. Direct interaction of K-259-2 and KS-619-1 with CaM was confirmed through use of hydrophobic fluorescent probes. Kinetic analysis revealed that the inhibition of the trypsin-activated phosphodiesterase was competitively inhibited by K-259-2 or KS-619-1 with respect to cAMP. Addition of a lower amount of either phosphatidylserine or sodium oleate to the reaction mixture was efficacious in attenuating the inhibition of the CaM-PDE by W-7, chlorpromazine, trifluoperazine, compound 48/80, or R-24571 but, in contrast, had little or no effect on the inhibition by K-259-2 or KS-619-1. In conclusion, K-259-2 and KS-619-1, unlike so-called CaM antagonists, do not interact with phosphatidylserine or sodium oleate and it appears that these novel anthraquinone compounds inhibit the enzyme not only via CaM antagonism but possibly also by interacting directly with the enzyme.