Abstract
Abelson kinase (Abl) is an enzyme crucial in metabolic pathways, and it is a molecular target for leukemias, especially chronic myeloid leukemia. Despite extensive research on its kinase function and inhibition over the years, there is still considerable room for new discoveries regarding its mechanistic and reactive aspects. We report here, for the first time, the intrinsic ATPase activity of Abl in the absence of peptide substrates. Using quantitative one-dimensional 31P nuclear magnetic resonance spectroscopy, we monitored the conversion of ATP to ADP and inorganic phosphate (Pi) catalyzed by Abl. Furthermore, we demonstrated that the known kinase inhibitors imatinib and dasatinib inhibit ATPase activity. Beyond expanding the biochemical repertoire of Abl, this finding enables a straightforward, substrate-free assay for kinase inhibition, offering new perspectives on kinase catalytic plasticity and laying the groundwork for simplified screening strategies in drug discovery.


1. Introduction
Protein kinases are central regulators of cellular signaling pathways; phosphoproteomic investigations indicate that the majority of proteins expressed in mammalian cells are subject to phosphorylation. Abelson kinase (Abl) is a well-studied human tyrosine kinase that plays a crucial role in cellular processes involved in DNA repair, cytoskeletal dynamics, and cellular apoptosis. − A dysregulation of these processes is related to different diseases, such as chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL). , Abl kinase intrigues researchers due to its multifaceted roles in cellular processes. Its modular architecture, comprising a kinase domain and regulatory SH2/SH3 domains, has been extensively studied. Conformational states, autoinhibition mechanisms, and ligand-induced activation have been resolved. −
Moreover, structural investigations have provided insights into the therapeutic mechanisms by revealing the binding modes of small-molecule inhibitors, such as imatinib and dasatinib, as well as the consequences of the binding process. Despite numerous studies on Abl and other tyrosine kinases, many aspects of their function, regulation, and interactions remain to be discovered. One example of a noncanonical activity of protein kinases is their potential ability to hydrolyze ATPreferred to as ATPase activity.
Here, we describe for the first time the intrinsic ATPase activity of full-length Abl kinase by tracking the conversion of ATP into ADP and inorganic phosphate (Pi) in the absence of any additional substrate. These findings add a new dimension to understanding its enzymatic repertoire, providing novel insights into its biochemical and cellular roles. Furthermore, we demonstrate that this activity can be leveraged to assess kinase inhibition by applying this method to CML-approved drugs.
2. Materials and Methods
2.1. 31P Quantitative NMR Experiments
To determine the phosphate concentration in solution, we created a calibration curve using seven solutions containing dibasic potassium phosphate (K2HPO4) concentrations ranging from 0 to 2 mM, performed in triplicate. The samples were prepared in a Tris-HCl 40 mM, pH 7.5 buffer, 2.5 mM MgCl2, 2% dimethyl sulfoxide (DMSO) (v/v), 11,7% D2O (v/v), and the K2HPO4 salt was prepared as described by Morita and Assumpção. The reaction in the presence of Abl was quenched by adding ethylenediaminetetraacetic acid (EDTA, 300 mM, pH 13) to a final concentration of 30 mM. Trimethyl phosphate (TMP) was used as an internal standard for quantification at a final concentration of 2.14 mM. The NMR experiments were conducted using a Bruker Avance III nanobay 400 MHz with a PABBFO-H-D/Z-grad 5 mm probe. The spectra were acquired with 65,536 points, a spectral window of 99.79 ppm, and 900 scans at 25 °C. Furthermore, a 60° pulse and a recovery time (D1) of 7 s were employed. The standard curve was determined by measuring the 31P NMR signal integral ratio of K2HPO4 to TMP (A Pi/A TMP) and plotted against the K2HPO4 concentration. Lastly, the spectra were processed and analyzed using Topspin 4.3.0 software (Bruker Corporation, USA).
Least-squares fitting was applied to the data and the coefficient of determination. The limits of detection (LOD) and quantification (LOQ) were determined based on calibration curves. Noise integration in the NMR spectra was performed over a 0.4 ppm range, matching the width used to integrate the phosphate signal in the calibration curve samples. The LOD and LOQ were then estimated using 20 noise regions in the NMR spectra. These values were obtained following standard methodology, where LOD is defined as 3.3 times the standard deviation of the noise (σ) divided by the slope (S) of the calibration curve (LOD = 3.3σ/S), and LOQ is defined as ten times the standard deviation of the noise divided by the slope (LOQ = 10σ/S). ,
2.2. Abl Kinase ATPase Activity Evaluation
Abl enzymatic reactions were performed at 20 °C in a reaction buffer with 40 mM Tris-HCl (pH 7.5), 2.5 mM magnesium chloride, 2% DMSO, and 11.7% D2O. After dilution, the final D2O concentration was 10%, allowing for frequency lock in NMR experiments. Reactions were initiated by adding ATP to a final concentration of 1.6 mM. The concentration of Abl kinase varied between 0 and 1.53 μM, depending on the aim of each experiment (further details on protein expression and purification are described in the Supporting Information). The final reaction volume was 605 μL. All reactions were quenched by adding the stop solution, an EDTA solution (300 mM, pH 13), to a final concentration of 30 mM. The TMP standard was also added to a final concentration of 2.14 mM. To evaluate the sensitivity of the Abl ATPase activity to the addition of known Abl kinase inhibitors, assays with imatinib and dasatinib were performed. Imatinib concentrations varied from 0 to 20 μM, while dasatinib was used at a fixed concentration of 3 μM. The enzyme was incubated for 10 min in the buffered solution with the inhibitors before ATP addition, and the reaction was stopped after 120 min.
2.3. Model Fitting and Analysis
The Pi concentration was estimated by applying the standard curve described in the section 2.1, and the time-course data were used to calculate the rate of phosphate production, which reflects ATP hydrolysis by Abl kinase. The enzymatic activity was expressed as k cat, in min–1, according to the following equation:
| 1 |
where ΔC prod is the change in phosphate concentration, Δt is the time interval, and [E]T is the enzyme concentration.
The percentage of inhibition (Inhibition %) of each inhibitor’s concentration was calculated using the following equation:
| 2 |
where C prod(without inhibitor) is the phosphate concentration in the reaction without inhibitor and C prod(with inhibitor) is the phosphate concentration in the presence of inhibitors.
The apparent dissociation constant (K d ) for imatinib binding to Abl was determined from the percentage of inhibition (Inhibition %) as a function of the total inhibitor concentration ([I]T). Data were acquired as percent inhibition versus [I]T at fixed enzyme and ATP concentrations ([E]T and [ATP], respectively). The analysis assumed a 1:1 binding stoichiometry (E + I ⇌ EI), in which the EI complex is catalytically inactive.
Because the ATPase reaction is a secondary process, a relatively high enzyme concentration ([E]T = 1.27 μM) was required to yield a detectable inorganic phosphate signal by 31P NMR within a reasonable experimental time frame. However, such high enzyme concentration invalidates the use of the classical Hill or Michaelis–Menten approximations, since the assumption [E]T ≪ K d no longer holds. Under these conditions, known as tight-binding inhibition, the free inhibitor concentration is substantially depleted upon enzyme binding, and a correction for this effect becomes mandatory. Therefore, the inhibition data were analyzed using the Morrison equation, which explicitly accounts for the stoichiometric binding of inhibitors by the enzyme. ,
At equilibrium, the fraction of enzyme present as EI (Fracinh) is expressed by the Morrison tight-binding equation using total concentrations
| 3 |
where [E]T and [I]T are the total enzyme and inhibitor concentrations, respectively, and K d is the apparent dissociation constant under the specific assay conditions.
The observed percentage of inhibition was modeled as
| 4 |
where I min and I max represent the lower and upper asymptotic limits of inhibition (typically 0% and 100%, respectively), accounting for potential baseline drift or incomplete inhibition.
For a competitive inhibitor in the presence of ATP, the apparent dissociation constant (K d ) relates to the intrinsic dissociation constant (K d) through a Cheng–Prusoff-like correction. ,
| 5 |
where [ATP] is the ATP concentration and K m the Michaelis constant for ATP binding to Abl. In this study, an ATP K m value of 43.6 μM, previously reported for Abl, was used to convert K d to the intrinsic K d.
Experimental inhibition data were fitted by nonlinear least-squares regression using the tight-binding model described above (eqs –). The fitting parameters were K d , I min, and I max, with the total enzyme concentration [E]T, and ATP K m of binding to Abl fixed at their nominal value. Confidence intervals (95%) were estimated from the covariance matrix of the fit. All data processing and regression analyses were performed using custom Python 3 scripts with SciPy 1.10.1 and NumPy 1.26 libraries, Microsoft Excel Office 2019, and OriginPro 2018.
3. Results and Discussion
3.1. Phosphate Formation Quantification by 31P Quantitative NMR Experiments
31P NMR is a robust and well-established method for quantifying inorganic phosphate (Pi), offering specificity and accuracy. The selectivity of 31P NMR eliminates signal overlap from other phosphorus-containing molecules, ensuring high-precision analysis of phosphate concentrations. This method has been extensively validated in the literature − and is widely used to study phosphate metabolism, , enzymatic reactions involving ATP, and phosphate transport kinetics. , Its high sensitivity, combined with the absence of overlapping signals from other phosphorus species, ensures reliable and unambiguous quantification of phosphate molecules.
To quantify the formation of Pi, we built a calibration curve by plotting the ratio of the 31P NMR signal integrals of Pi and TMP as a function of known phosphate concentrations (Figure ). A linear correlation was observed for the Pi concentrations, with an r 2 value of 0.998. The limits of detection (LOD) and quantification (LOQ) were calculated to be 40.3 μM and 122 μM, respectively.
1.
Calibration curve for phosphate quantification by 31P NMR. Samples containing increasing concentrations of phosphate were prepared in 40 mM Tris-HCl buffer (pH 7.5) with 2.5 mM MgCl2, 2% v/v DMSO, and 2.14 mM trimethyl phosphate (TMP) as internal standard. Data represents the average of experiments performed in triplicate.
3.2. Abl ATPase Activity Discovery
Employing the full-length Abl kinase and quantitative one-dimensional 31P NMR spectroscopy, we monitored changes in the NMR signals of ATP, ADP, and Pi. The quantitative protocol was adapted from Lajoie et al. and used to evaluate the consumption of ATP and the formation of ADP and Pi. The addition of 1.27 μM Abl kinase into a system containing 1.6 mM ATP induced ATP hydrolysis, as indicated by a decrease in the β-ATP signal (−21.6 ppm) and an increase in the Pi signal (2.5 ppm), as well as changes in the α and β phosphate groups of ADP, as observed in the spectra (Figure , red colored spectrum). The conversion of ATP into ADP was monitored using TMP as an internal standard to calibrate ADP and ATP NMR signals and quantify their concentrations. ATP hydrolysis was not observed in a system lacking Abl (Figure , blue spectrum).
2.
Monitoring ATP hydrolysis by quantitative 31P NMR. (a) Schematic representation of ATP hydrolysis. (b) 31P NMR spectra. The reaction medium consisted of 40 mM Tris-HCl buffer (pH 7.5), 2.5 mM magnesium chloride, and 2% v/v DMSO. The red spectrum corresponds to the reaction medium containing 1.27 μM Abl enzyme, while the blue spectrum represents the control medium without enzyme, showing no reaction. Reactions were initiated by adding ATP to a final concentration of 1.6 mM, incubated for 2 h, and then quenched with EDTA prior to 31P NMR analysis.
Control experiments confirmed the specificity of the Abl ATPase activity. In Abl’s absence, no spontaneous ATP conversion was observed even after 17 h of incubation. This can be visualized in the NMR spectra, where the ATP signals intensity were conserved (Supporting Information Section 2–ATP Stability Under the Assay Condition). Additionally, we investigate the possible contamination of the reaction solution with spurious phosphatases in the purified Abl samples, as such enzymes could trigger the Abl dephosphorylation and, consequently, the formation of Pi by alternative routes. Two distinct methodologies were employed to ensure the absence of phosphatase contamination. Initially, an SDS-PAGE analysis of the Abl samples was performed, and no additional bands were detected beyond those expected for the molecular weight of Abl kinase. Subsequently, para-nitrophenyl phosphate (pNPP), a known phosphatase substrate, was added to the samples. The hydrolysis product, para-nitrophenol, exhibits a yellow coloration, which can be monitored by UV–vis spectroscopy, in contrast to the colorless pNPP. , When applied to the Abl sample, no hydrolysis of pNPP was observed. These findings demonstrate that the purified Abl kinase was free from phosphatase contamination (Supporting Information Section 3Phosphatase Contamination Assay to Confirm Purity of Abl Kinase Preparation).
ATPase activity has been identified in a few kinases, such as Src, cAMP-dependent protein kinase, extracellular signal-regulated kinase 2 (ERK2), and protein kinase C (PKC). In the study by Rominger and colleagues, it was observed that MEK lacks detectable ATPase activity unless phosphorylated by upstream Raf kinases. Upon phosphorylation, MEK catalyzes robust ATP hydrolysis even in the absence of its substrate, ERK, indicating an intrinsic ATPase activity under specific activation conditions. This observation suggests an additional regulatory layer in MEK function and contributes to the limited but growing body of evidence that some kinases may display enzymatic activities beyond their canonical role in substrate phosphorylation. Despite sporadic reports in the literature, this area remains largely underexplored.
3.3. Abl ATPase Activity as a Proxy for Kinase Activity
The observed linear correlation between the initial velocity of phosphate formation and the Abl concentration (Figure a) is itself diagnostic of saturating substrate conditions. This interpretation is supported by the fact that the ATP concentration used (1.6 mM) was approximately 30-fold higher than its K m value of 43.6 μM.147 As per the Michaelis–Menten equation, v 0 = k cat[E]t([S]/(K m + [S])), when [S] ≫ K m, the term [S]/(K m + [S]) approaches unity, simplifying the relationship to v0 ≈ k cat[E]t. Under these conditions, the velocity depends linearly on the enzyme concentration, and the slope of this relationship yields the k cat. Our data demonstrate this linear dependence, showing that we are measuring the maximal catalytic rate (v max) for each enzyme concentration. Consequently, the ATPase activity of Abl can be reliably monitored under these saturating conditions, making it a valid system for inhibitor screening.
3.

Development of an Abl assay based on ATPase activity. (a) Kinetic characterization of Abl ATPase activity by 1D 31P NMR. Reactions were carried out in 40 mM Tris-HCl buffer (pH 7.5), containing 2.5 mM MgCl2 and 2% v/v DMSO, initiated by the addition of ATP (final concentration: 2.58 mM). Abl was added to the reaction medium, which was incubated at 20 °C for 2 h and then quenched with EDTA. Reaction progress was monitored by 1D 31P NMR, using TMP (final concentration: 2.14 mM) as an internal standard. (b) Effect of imatinib concentration on Abl activity, assessed by 1D 31P NMR under identical buffer conditions. Abl (1.27 μM) was incubated with ATP (1.61 mM) at 20 °C for 2 h before quenching with EDTA and NMR analysis. TMP (2.14 mM) served as an internal reference. (c) Comparison of imatinib and dasatinib (3 μM each) on Abl activity. Reactions were performed as described above, with TMP (2.14 mM) as internal standard.
From these data, the turnover number (k cat) of (5.3 ± 0.2) min–1 (8.8 × 10–2 s–1) was obtained. Despite being significantly smaller than an ideal substrate, such as abltide (a peptide optimized for Abl kinase described by Songyang et al.), we were able to use this reaction to measure ATP consumption as a feature for the assay. Compared to the kinase domain turnover number, we observed that the ATP hydrolysis rate is approximately 80 times lower than that reported for abltide. Nevertheless, this was expected, as it is a background reaction. The observation is consistent with previous studies on the ATPase activity of other kinases, which have generally been found to be much slower than their phosphotransferase activity. ,
Comparing the ATPase activity with that of other kinases, such as the rabbit skeletal muscle phosphorylase kinase, this activity occurs at approximately 0.2% of the rate of its phosphoryl transfer activity and is three times slower than its autophosphorylation activity. Another example is the ATPase activity of Protein Kinase C (PKC) isoforms found in rat brains. Under assay conditions, the ATPase activity of the purified PKC-α and PKC-γ isoforms was 4.7% and 2.6% of the kinase activity, respectively. PKC-α hydrolyzed ATP at (0.085 ± 0.020) pmol·min–1, while its kinase activity was (1.80 ± 0.08) pmol·min–1. Similarly, PKC-γ exhibited ATP hydrolysis rates of 0.061 ± 0.018 pmol·min–1 and kinase activity of (2.34 ± 0.27) pmol·min–1. Our data align with observations for other protein kinases, corroborating ATPase activity as a background reaction. This lower level of ATP hydrolysis prevents unnecessary substrate consumption while maintaining the primary physiological function of the kinase.
ATP hydrolysis by PKC occurs at the active site, as demonstrated by Ward and O’Brian. Their findings indicate that both ATPase and catalytic activities occur at the orthosteric site, supported by apparent ATP K m values observed across different isoforms. The link between ATPase and kinase activity inhibition was confirmed for hexokinases through a systematic assessment of both activities in the presence of various inhibitors, clarifying the relationship between these enzymatic functions. For instance, 3 mM N-(m-nitrobenzoyl)-d-glucosamine inhibited 51.8% of kinase activity in the presence of the substrate, whereas in its absence, it inhibited 80.5% of ATPase activity. We applied a similar approach to assess the Abl ATPase activity in the presence of kinase inhibitors. We tested it using imatinib and dasatinib, which are competitive inhibitors targeting the ATP binding site of Abl. We hypothesized that these inhibitors could also suppress ATPase activity, reflecting their ability to inhibit kinase activity.
The enzyme inhibition data for imatinib against Abl kinase were analyzed using the Morrison tight-binding equation. This approach was necessitated by the experimental conditions, where the total enzyme concentration ([E]T) was not negligible compared to the inhibitor concentration ([I]T), thereby invalidating the assumptions underlying classical Michaelis–Menten or Hill approximations. , The Morrison formalism accounts for the significant depletion of the free inhibitor by the enzyme, providing a more accurate determination of the dissociation constant under these conditions. From this analysis, a K d value of 67 nM was determined. This result is near to reported values in the literature 8 nM and 26 nM.
This experimentally derived K d of 67 nM occupies an intermediate position within the range of values reported in the literature, which spans from 3.8 nM to 140 nM. A plausible explanation for this intermediate value lies in the phosphorylation status of Abl kinase during the assay. The present study measured ATPase activity under kinetic conditions in the presence of ATP. Consequently, the enzyme, initially in a dephosphorylated state, may be progressively phosphorylated throughout the reaction course. Given that Manley et al. demonstrated an influence of phosphorylation status on imatinib affinityreporting a K d of 3.8 nM for the nonphosphorylated form and 141 nM for the phosphorylated formthe observed value of 67 nM likely represents a population-weighted average. It reflects the dynamic equilibrium between the high-affinity (dephosphorylated) and low-affinity (phosphorylated) states of Abl kinase present in the reaction mixture, thereby reconciling our result with the existing literature.
A comparative analysis between imatinib and dasatinib at an equimolar concentration of 3 μM demonstrated different inhibitory profiles (Figure c): while imatinib inhibited approximately 50% of the enzymatic activity, dasatinib achieved complete inhibition under the same conditions. This pronounced difference is consistent with the known higher binding affinity of dasatinib for Abl kinase, reflecting its more potent inhibitory capacity.
It is important to consider the specific limitations of the ATPase-based assay employed in this study. This method detects inhibition by measuring the decrease in the intrinsic ATP hydrolysis rate of Abl. Consequently, its applicability is inherently linked to the mechanism of action of the inhibitor. The assay is expected to be effective for compounds that directly compete with ATP binding (Type I and II inhibitors) or allosteric inhibitors that stabilize an inactive conformation, thereby impairing the catalytic apparatus necessary for phosphate transfer. However, this approach may fail to identify certain classes of inhibitors. For instance, compounds that bind exclusively to the substrate peptide-binding site without impeding ATP binding or the nucleophilic attack by water would likely not inhibit the observed ATPase activity. Similarly, allosteric inhibitors that do not lock the enzyme in a specific conformation or otherwise affect the catalytic steps of ATP binding and hydrolysis may also remain undetected. Therefore, while this ATPase assay provides a valuable and direct functional readout for a specific subset of kinase inhibitors, it is not a universal screening method, and its results should be interpreted within this mechanistic context.
The usage of 31P NMR is relatively expensive, and its accessibility may be limited in some settings. However, the discovery of Abl ATPase activity opens new opportunities to combine this finding with other established methods for measuring inorganic phosphate (Pi), potentially simplifying and enhancing current analytical pipelines. Among these alternative methods, those based on the molybdenum blue reaction are particularly promising. This approach, which relies on forming a phosphomolybdenum blue complex, is highly sensitive and has been widely employed for the determination of orthophosphate in environmental samples. This strategy stands out for its high sensitivity, operational simplicity, and compatibility with spectrophotometric analyses in the visible region.
Also, electroanalytical methods are another potential strategy that could be coupled with ATPase activity. Sensors based on modified electrodes, metal complexes, and supramolecular systems may enable selective phosphate recognition, offering stability and reducing interference compared to optical techniques, while also facilitating miniaturization, real-time analysis, and portability. Modulating the Pi chemical equilibrium to promote strong binding to hard metal cations has been explored as a means to develop sensors for the rapid, simple, and reliable detection of phosphate species, such as those based on europium, terbium, and copper complexes. Finally, ion chromatography, renowned for its high sensitivity, is a powerful technique for phosphate analysis, proving to be another efficient approach. ,
4. Conclusions
Here, we show the kinetic profile of Abl’s intrinsic ATPase activity, which led to the development of an ATPase activity-based assay for Abl kinase. Although the ATPase activity observed for Abl is significantly slower than its canonical phosphotransferase function, it uncovers a noncanonical enzymatic behavior with potential mechanistic and analytical implications. Reports of similar basal ATPase activities in other kinases, such as SRC, PKC, and ERK2, suggest that this may be a conserved yet underexplored feature of the kinase superfamily. It is plausible that such residual ATP hydrolysis reflects intrinsic conformational fluctuations at the active sitepossibly linked to autoinhibition dynamics or catalytic resetting. From a practical perspective, we show that this ATPase activity is inhibited by ATP-competitive drugs, validating its use as a proxy for kinase inhibition. This enables the development of substrate-free assays that dispense with peptides, other enzymes, or radiolabels, offering a simplified and scalable strategy for kinase inhibitor screening. Thus, the discovery of Abl’s intrinsic ATPase activity not only expands our biochemical understanding of this key therapeutic target but also provides a foundation for novel assay formats with translational utility.
Supplementary Material
Acknowledgments
We thank FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais), FINEP (Brazilian Innovation and Research Funding Agency), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) for financial support. We also thank the “Laboratório de Ressonância Magnética de Alta Resolução da UFMG” (LAREMAR) for providing the NMR infrastructure. We are grateful to Prof. Dr. Stephan Grzesiek (Biozentrum, University of Basel) for kindly providing the Abl kinase plasmid.
Glossary
Abbreviations
- Abl
Abelson kinase
- ADP
adenosine diphosphate
- ATP
adenosine triphosphate
- ALL
acute lymphoblastic leukemia
- Bcr
breakpoint cluster region
- CML
chronic Myeloid leukemia
- DMSO
dimethyl sulfoxide
- EDTA
ethylenediaminetetraacetic acid
- ERK2
extracellular signal-regulated kinase 2
- K d
dissociation constant
- LOD
limit of detection
- LOQ
limit of quantification
- MEK
mitogen-activated protein kinase
- NMR
nuclear magnetic resonance
- pNPP
para-nitrophenyl phosphate
- PKC
protein kinase C
- Pi
inorganic phosphate
- SDS-PAGE
sodium dodecyl sulfate polyacrylamide gel electrophoresis
- SH2
Src homology 2 domain
- SH3
Src homology 3 domain
- SRC
proto-oncogene tyrosine-protein kinase
- TMP
trimethyl phosphate
- UV–vis
ultraviolet–visible spectroscopy
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsomega.5c08176.
Experimental details regarding protein expression and purification, ATP stability assays, and tests for phosphatase activity detection (PDF)
∥.
D.M.M. and P.O.F. contributed equally to this work. D.M.M. and L.A.V. caried out protein expression and purification. D.M.M. performed NMR experiments. D.M.M. and P.O.F. performed formal analysis on the acquired data. A.H.M. and T.A.B. conceptualized the experimental design and supervised the experiments. A.H.M. provided resources and acquired funding. D.M.M. and P.O.F. designed the charts and figures and prepared the original draft.
The Article Processing Charge for the publication of this research was funded by the Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES), Brazil (ROR identifier: 00x0ma614).
FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais) grant number: 001/2022DEMANDA UNIVERSAL/Processo: APQ-00428–2, FINEP (Brazilian Innovation and Research Funding Agency), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico).
The authors declare no competing financial interest.
Published as part of ACS Omega special issue “Chemistry in Brazil: Advancing through Open Science”.
References
- Olsen J. V., Vermeulen M., Santamaria A., Kumar C., Miller M. L., Jensen L. J., Gnad F., Cox J., Jensen T. S., Nigg E. A., Brunak S., Mann M.. Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis. Sci. Signaling. 2010;3(104):ra3. doi: 10.1126/scisignal.2000475. [DOI] [PubMed] [Google Scholar]
- Kharbanda S., Yuan Z.-M., Weichselbaum R., Kufe D.. Determination of Cell Fate by C-Abl Activation in the Response to DNA Damage. Oncogene. 1998;17(25):3309–3318. doi: 10.1038/sj.onc.1202571. [DOI] [PubMed] [Google Scholar]
- Huang Y., Comiskey E. O., Dupree R. S., Li S., Koleske A. J., Burkhardt J. K.. The C-Abl Tyrosine Kinase Regulates Actin Remodeling at the Immune Synapse. Blood. 2008;112(1):111–119. doi: 10.1182/blood-2007-10-118232. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schlatterer S. D., Acker C. M., Davies P.. C-Abl in Neurodegenerative Disease. J. Mol. Neurosci. 2011;45(3):445–452. doi: 10.1007/s12031-011-9588-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Aoyama K., Fukumoto Y., Ishibashi K., Kubota S., Morinaga T., Horiike Y., Yuki R., Takahashi A., Nakayama Y., Yamaguchi N.. Nuclear C-Abl-Mediated Tyrosine Phosphorylation Induces Chromatin Structural Changes through Histone Modifications That Include H4K16 Hypoacetylation. Exp. Cell Res. 2011;317(20):2874–2903. doi: 10.1016/j.yexcr.2011.09.013. [DOI] [PubMed] [Google Scholar]
- Mahajan K., Mahajan N. P.. Cross Talk of Tyrosine Kinases with the DNA Damage Signaling Pathways. Nucleic Acids Res. 2015;43(22):10588–10601. doi: 10.1093/nar/gkv1166. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang J. Y. J.. The Capable ABL: What Is Its Biological Function? Mol. Cell. Biol. 2014;34(7):1188–1197. doi: 10.1128/MCB.01454-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Greuber E. K., Smith-Pearson P., Wang J., Pendergast A. M.. Role of ABL Family Kinases in Cancer: From Leukaemia to Solid Tumours. Nat. Rev. Cancer. 2013;13(8):559–571. doi: 10.1038/nrc3563. [DOI] [PMC free article] [PubMed] [Google Scholar]
- An X., Tiwari A. K., Sun Y., Ding P.-R., Ashby C. R., Chen Z.-S.. BCR-ABL Tyrosine Kinase Inhibitors in the Treatment of Philadelphia Chromosome Positive Chronic Myeloid Leukemia: A Review. Leuk. Res. 2010;34(10):1255–1268. doi: 10.1016/j.leukres.2010.04.016. [DOI] [PubMed] [Google Scholar]
- Nagar B., Hantschel O., Seeliger M., Davies J. M., Weis W. I., Superti-Furga G., Kuriyan J.. Organization of the SH3-SH2 Unit in Active and Inactive Forms of the c-Abl Tyrosine Kinase. Mol. Cell. 2006;21(6):787–798. doi: 10.1016/j.molcel.2006.01.035. [DOI] [PubMed] [Google Scholar]
- Nagar B., Hantschel O., Young M. A., Scheffzek K., Veach D., Bornmann W., Clarkson B., Superti-Furga G., Kuriyan J.. Structural Basis for the Autoinhibition of C-Abl Tyrosine Kinase. Cell. 2003;112(6):859–871. doi: 10.1016/S0092-8674(03)00194-6. [DOI] [PubMed] [Google Scholar]
- Hantschel O., Nagar B., Guettler S., Kretzschmar J., Dorey K., Kuriyan J., Superti-Furga G.. A Myristoyl/Phosphotyrosine Switch Regulates c-Abl. Cell. 2003;112(6):845–857. doi: 10.1016/S0092-8674(03)00191-0. [DOI] [PubMed] [Google Scholar]
- Brasher B. B., Etten R. A. V.. C-Abl Has High Intrinsic Tyrosine Kinase Activity That Is Stimulated by Mutation of the Src Homology 3 Domain and by Autophosphorylation at Two Distinct Regulatory Tyrosines. J. Biol. Chem. 2000;275(45):35631–35637. doi: 10.1074/jbc.M005401200. [DOI] [PubMed] [Google Scholar]
- Saleh T., Rossi P., Kalodimos C. G.. Atomic View of the Energy Landscape in the Allosteric Regulation of Abl Kinase. Nat. Struct Mol. Biol. 2017;24(11):893–901. doi: 10.1038/nsmb.3470. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sonti R., Hertel-Hering I., Lamontanara A. J., Hantschel O., Grzesiek S.. ATP Site Ligands Determine the Assembly State of the Abelson Kinase Regulatory Core via the Activation Loop Conformation. J. Am. Chem. Soc. 2018;140(5):1863–1869. doi: 10.1021/jacs.7b12430. [DOI] [PubMed] [Google Scholar]
- Martins D. M., Fernandes P. O., Vieira L. A., Maltarollo V. G., Moraes A. H.. Structure-Guided Drug Design Targeting Abl Kinase: How Structure and Regulation Can Assist in Designing New Drugs. ChemBioChem. 2024;25(23):e202400296. doi: 10.1002/cbic.202400296. [DOI] [PubMed] [Google Scholar]
- Roskoski R.. Targeting BCR-Abl in the Treatment of Philadelphia-Chromosome Positive Chronic Myelogenous Leukemia. Pharmacol. Res. 2022;178:106156. doi: 10.1016/j.phrs.2022.106156. [DOI] [PubMed] [Google Scholar]
- Morita, T. ; Assumpção, R. M. V. . Manual de Soluções, Reagentes e Solventes: Padronização, Preparação, Purificação, Indicadores de Segurança e Descarte de Produtos Químicos; Ed.a Blucher, 2007. [Google Scholar]
- Soininen P., Haarala J., Vepsäläinen J., Niemitz M., Laatikainen R.. Strategies for Organic Impurity Quantification by 1H NMR Spectroscopy: Constrained Total-Line-Shape Fitting. Anal. Chim. Acta. 2005;542(2):178–185. doi: 10.1016/j.aca.2005.03.060. [DOI] [Google Scholar]
- Zhao J., Wang M., Avula B., Khan I. A.. Detection and Quantification of Phenethylamines in Sports Dietary Supplements by NMR Approach. J. Pharm. Biomed. Anal. 2018;151:347–355. doi: 10.1016/j.jpba.2018.01.025. [DOI] [PubMed] [Google Scholar]
- Morrison J. F.. Kinetics of the Reversible Inhibition of Enzyme-Catalysed Reactions by Tight-Binding Inhibitors. Biochim. Biophys. Acta, Enzymol. 1969;185(2):269–286. doi: 10.1016/0005-2744(69)90420-3. [DOI] [PubMed] [Google Scholar]
- Srinivasan B.. Explicit Treatment of Non-Michaelis-Menten and Atypical Kinetics in Early Drug Discovery**. ChemMedChem. 2021;16(6):899–918. doi: 10.1002/cmdc.202000791. [DOI] [PubMed] [Google Scholar]
- Yen Y.-C., Kammeyer A. M., Jensen K. C., Tirlangi J., Ghosh A. K., Mesecar A. D.. Development of an Efficient Enzyme Production and Structure-Based Discovery Platform for BACE1 Inhibitors. Biochemistry. 2019;58(44):4424–4435. doi: 10.1021/acs.biochem.9b00714. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yung-Chi C., Prusoff W. H.. Relationship between the Inhibition Constant (Ki) and the Concentration of Inhibitor Which Causes 50 per Cent Inhibition (IC50) of an Enzymatic Reaction. Biochem. Pharmacol. 1973;22(23):3099–3108. doi: 10.1016/0006-2952(73)90196-2. [DOI] [PubMed] [Google Scholar]
- Williams, J. W. ; Morrison, J. F. . [17] The Kinetics of Reversible Tight-Binding Inhibition. In Methods in Enzymology; Elsevier, 1979; Vol. 63, pp 437–467 10.1016/0076-6879(79)63019-7. [DOI] [PubMed] [Google Scholar]
- Chen H., Adams E., Van Schepdael A.. LC–ESI–MS Method for the Monitoring of Abl 1 Tyrosine Kinase. J. Chromatogr. B. 2012;897:17–21. doi: 10.1016/j.jchromb.2012.04.001. [DOI] [PubMed] [Google Scholar]
- Lajoie D. M., Zobel-Thropp P. A., Kumirov V. K., Bandarian V., Binford G. J., Cordes M. H. J.. Phospholipase D Toxins of Brown Spider Venom Convert Lysophosphatidylcholine and Sphingomyelin to Cyclic Phosphates. PLoS One. 2013;8(8):e72372. doi: 10.1371/journal.pone.0072372. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Daly P. F., Lyon R. C., Faustino P. J., Cohen J. S.. Phospholipid Metabolism in Cancer Cells Monitored by 31P NMR Spectroscopy. J. Biol. Chem. 1987;262(31):14875–14878. doi: 10.1016/S0021-9258(18)48107-0. [DOI] [PubMed] [Google Scholar]
- Cunha L. C., Valadares V. S., De Oliveira J. S., Felicori L. F., Moraes A. H.. Standardization of Lipid Sample Preparation for Monitoring Phospholipase Activity. Arch. Biochem. Biophys. 2025;768:110373. doi: 10.1016/j.abb.2025.110373. [DOI] [PubMed] [Google Scholar]
- Kuesel A. C., Stoyanova R., Aiken N. R., Li C.-W., Szwergold B. S., Shaller C., Brown T. R.. Quantitation of Resonances in Biological 31P NMR Spectra via Principal Component Analysis: Potential and Limitations. NMR Biomed. 1996;9(3):93–104. doi: 10.1002/(SICI)1099-1492(199605)9:3<93::AID-NBM410>3.0.CO;2-D. [DOI] [PubMed] [Google Scholar]
- Godinot C., Gaysinski M., Thomas O. P., Ferrier-Pagès C., Grover R.. On the Use of 31P NMR for the Quantification of Hydrosoluble Phosphorus-Containing Compounds in Coral Host Tissues and Cultured Zooxanthellae. Sci. Rep. 2016;6(1):21760. doi: 10.1038/srep21760. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Escobedo-Hinojosa W., Wissner J. L., Hauer B.. A Real-Time 31P-NMR-Based Approach for the Assessment of Glycerol Kinase Catalyzed Monophosphorylations. MethodsX. 2021;8:101285. doi: 10.1016/j.mex.2021.101285. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bourne R. M.. A 31P-NMR Study of Phosphate Transport and Compartmentation in Candida utilis. Biochim. Biophys. Acta, Mol. Cell Res. 1990;1055(1):1–9. doi: 10.1016/0167-4889(90)90084-Q. [DOI] [PubMed] [Google Scholar]
- Nardi-Schreiber A., Gamliel A., Harris T., Sapir G., Sosna J., Gomori J. M., Katz-Brull R.. Biochemical Phosphates Observed Using Hyperpolarized 31P in Physiological Aqueous Solutions. Nat. Commun. 2017;8(1):341. doi: 10.1038/s41467-017-00364-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brandão T. A. S., Hengge A. C., Johnson S. J.. Insights into the Reaction of Protein-Tyrosine Phosphatase 1B: Crystal Structures for Transition State Analogs of Both Catalytic Steps. J. Biol. Chem. 2010;285(21):15874–15883. doi: 10.1074/jbc.M109.066951. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brandão T. A., Johnson S. J., Hengge A. C.. The Molecular Details of WPD-Loop Movement Differ in the Protein-Tyrosine Phosphatases YopH and PTP1B. Arch. Biochem. Biophys. 2012;525(1):53–59. doi: 10.1016/j.abb.2012.06.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kim D., Sun Y., Xie D., Denton K. E., Chen H., Lin H., Wendt M. K., Post C. B., Krusemark C. J.. Application of a Substrate-Mediated Selection with c-Src Tyrosine Kinase to a DNA-Encoded Chemical Library. Molecules. 2019;24(15):2764. doi: 10.3390/molecules24152764. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mendelow M., Prorok M., Salerno A., Lawrence D. S.. ATPase-Promoting Dead End Inhibitors of the cAMP-Dependent Protein Kinase. J. Biol. Chem. 1993;268(17):12289–12296. doi: 10.1016/S0021-9258(18)31387-5. [DOI] [PubMed] [Google Scholar]
- Prowse C. N., Lew J.. Mechanism of Activation of ERK2 by Dual Phosphorylation *. J. Biol. Chem. 2001;276(1):99–103. doi: 10.1074/jbc.M008137200. [DOI] [PubMed] [Google Scholar]
- Ward N. E., O’Brian C. A.. The Intrinsic ATPase Activity of Protein Kinase C Is Catalyzed at the Active Site of the Enzyme. Biochemistry. 1992;31(25):5905–5911. doi: 10.1021/bi00140a029. [DOI] [PubMed] [Google Scholar]
- Rominger C. M., Schaber M. D., Yang J., Gontarek R. R., Weaver K. L., Broderick T., Carter L., Copeland R. A., May E. W.. An Intrinsic ATPase Activity of Phospho-MEK-1 Uncoupled from Downstream ERK Phosphorylation. Arch. Biochem. Biophys. 2007;464(1):130–137. doi: 10.1016/j.abb.2007.04.004. [DOI] [PubMed] [Google Scholar]
- Songyang Z., Carraway K. L., Eck M. J., Harrison S. C., Feldman R. A., Mohammadi M., Schlessinger J., Hubbard S. R., Smith D. P., Eng C., Lorenzo M. J., Ponder B. A. J., Mayer B. J., Cantley L. C.. Catalytic Specificity of Protein-Tyrosine Kinases Is Critical for Selective Signalling. Nature. 1995;373(6514):536–539. doi: 10.1038/373536a0. [DOI] [PubMed] [Google Scholar]
- Li F., Fahie M. A., Gilliam K. M., Pham R., Chen M.. Mapping the Conformational Energy Landscape of Abl Kinase Using ClyA Nanopore Tweezers. Nat. Commun. 2022;13(1):3541. doi: 10.1038/s41467-022-31215-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang Y., Hanrahan G., Abou Azar F., Mittermaier A.. Binding Interactions in a Kinase Active Site Modulate Background ATP Hydrolysis. Biochim. Biophys. Acta, Proteins Proteomics. 2022;1870(1):140720. doi: 10.1016/j.bbapap.2021.140720. [DOI] [PubMed] [Google Scholar]
- Paudel H. K., Carlson G. M.. The ATPase Activity of Phosphorylase Kinase Is Regulated in Parallel with Its Protein Kinase Activity. J. Biol. Chem. 1991;266(25):16524–16529. doi: 10.1016/S0021-9258(18)55332-1. [DOI] [PubMed] [Google Scholar]
- Kaji A., Colowick S. P.. Adenosine Triphosphatase Activity of Yeast Hexokinase and Its Relation to the Mechanism of the Hexokinase Reaction. J. Biol. Chem. 1965;240(11):4454–4462. doi: 10.1016/S0021-9258(18)97083-3. [DOI] [PubMed] [Google Scholar]
- Andretta E., Costa C., Longobardi C., Damiano S., Giordano A., Pagnini F., Montagnaro S., Quintiliani M., Lauritano C., Ciarcia R.. Potential Approaches Versus Approved or Developing Chronic Myeloid Leukemia Therapy. Front. Oncol. 2021;11:801779. doi: 10.3389/fonc.2021.801779. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lyczek A., Berger B.-T., Rangwala A. M., Paung Y., Tom J., Philipose H., Guo J., Albanese S. K., Robers M. B., Knapp S., Chodera J. D., Seeliger M. A.. Mutation in Abl Kinase with Altered Drug-Binding Kinetics Indicates a Novel Mechanism of Imatinib Resistance. Proc. Natl. Acad. Sci. U.S.A. 2021;118(46):e2111451118. doi: 10.1073/pnas.2111451118. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hoemberger M., Pitsawong W., Kern D.. Cumulative Mechanism of Several Major Imatinib-Resistant Mutations in Abl Kinase. Proc. Natl. Acad. Sci. U.S.A. 2020;117(32):19221–19227. doi: 10.1073/pnas.1919221117. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hari S. B., Perera B. G. K., Ranjitkar P., Seeliger M. A., Maly D. J.. Conformation-Selective Inhibitors Reveal Differences in the Activation and Phosphate-Binding Loops of the Tyrosine Kinases Abl and Src. ACS Chem. Biol. 2013;8(12):2734–2743. doi: 10.1021/cb400663k. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Manley P. W., Cowan-Jacob S. W., Fendrich G., Jahnke W., Fabbro D.. Nilotinib, in Comparison to Both Dasatinib and Imatinib, Possesses a Greatly Prolonged Residence Time When Bound to the BCR-ABL Kinase SH1 Domain. Blood. 2011;118(21):1674. doi: 10.1182/blood.V118.21.1674.1674. [DOI] [Google Scholar]
- Rix U., Hantschel O., Dürnberger G., Rix L. L. R., Planyavsky M., Fernbach N. V., Kaupe I., Bennett K. L., Valent P., Colinge J., Köcher T., Superti-Furga G.. Chemical Proteomic Profiles of the BCR-ABL Inhibitors Imatinib, Nilotinib, and Dasatinib Reveal Novel Kinase and Nonkinase Targets. Blood. 2007;110(12):4055–4063. doi: 10.1182/blood-2007-07-102061. [DOI] [PubMed] [Google Scholar]
- Nagul E. A., McKelvie I. D., Worsfold P., Kolev S. D.. The Molybdenum Blue Reaction for the Determination of Orthophosphate Revisited: Opening the Black Box. Anal. Chim. Acta. 2015;890:60–82. doi: 10.1016/j.aca.2015.07.030. [DOI] [PubMed] [Google Scholar]
- Berchmans S., Issa T. B., Singh P.. Determination of Inorganic Phosphate by Electroanalytical Methods: A Review. Anal. Chim. Acta. 2012;729:7–20. doi: 10.1016/j.aca.2012.03.060. [DOI] [PubMed] [Google Scholar]
- Krämer J., Kang R., Grimm L. M., De Cola L., Picchetti P., Biedermann F.. Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids. Chem. Rev. 2022;122(3):3459–3636. doi: 10.1021/acs.chemrev.1c00746. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Buldini P. L., Cavalli S., Sharma J. L.. Matrix Removal for the Ion Chromatographic Determination of Some Trace Elements in Milk. Microchem. J. 2002;72(3):277–284. doi: 10.1016/S0026-265X(02)00039-5. [DOI] [Google Scholar]
- Quintana J. B., Rodil R., Reemtsma T.. Determination of Phosphoric Acid Mono- and Diesters in Municipal Wastewater by Solid-Phase Extraction and Ion-Pair Liquid Chromatography–Tandem Mass Spectrometry. Anal. Chem. 2006;78(5):1644–1650. doi: 10.1021/ac0517186. [DOI] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.


