Active site profiling reveals coupling between domains in SRC-family kinases.

Protein kinases, key regulators of intracellular signal transduction, have emerged as an important class of drug targets. Chemical proteomic tools that facilitate the functional interrogation of protein kinase active sites are powerful reagents for studying the regulation of this large enzyme family and performing inhibitor selectivity screens. Here we describe a new crosslinking strategy that enables rapid and quantitative profiling of protein kinase active sites in lysates and live cells. Applying this methodology to the SRC-family kinases (SFKs) SRC and HCK led to the identification of a series of conformation-specific, ATP-competitive inhibitors that have a distinct preference for the autoinhibited forms of these kinases. Furthermore, we show that ligands that have this selectivity are able to modulate the ability of the regulatory domains of SRC and HCK to engage in intermolecular binding interactions. These studies provide insight into the regulation of this important family of tyrosine kinases.

Affinity-based probes based on type II kinase inhibitors.

Protein kinases are key components of most mammalian signal transduction networks and are therapeutically relevant drug targets. Efforts to study protein kinase function would benefit from new technologies that are able to profile kinases in complex proteomes. Here, we describe active site-directed probes for profiling kinases in whole cell extracts and live cells. These probes contain general ligands that stabilize a specific inactive conformation of the ATP-binding sites of protein kinases, as well as trifluoromethylphenyl diazirine and alkyne moieties that allow covalent modification and enrichment of kinases, respectively. A diverse group of serine/threonine and tyrosine kinases were identified as specific targets of these probes in whole cell extracts. In addition, a number of kinase targets were selectively labeled in live cells. Our chemical proteomics approach should be valuable for interrogating protein kinase active sites in physiologically relevant environments.

Small volume retinol binding protein measurement by liquid chromatography-tandem mass spectrometry.

BACKGROUND: The measurement of plasma concentrations of retinol binding protein is a component of nutritional assessment in neonatal intensive care. However, serial testing in newborns is hampered by the limited amount of blood that can be sampled. Limitations are most severe with preterm infants, for whom close monitoring may be most important. METHODS: We developed an assay to quantify retinol binding protein using trypsin digestion and liquid chromatography-tandem mass spectrometry, which requires a serum or plasma volume of 5 µl. Additionally, we validated the method according to current recommendations and performed comparison with a standard nephelometry platform in clinical use. RESULTS: The assay demonstrated linearity from below 1 mg/dL (0.48 µM) to more than 20 mg/dL (9.7 µM), and an imprecision of 11.8% at 0.43 mg/dL (0.21 µM). The distribution of results observed with the new method was different when compared with nephelometry. CONCLUSION: Liquid chromatography-tandem mass spectrometry facilitated testing a smaller sample volume, thereby increasing the ability to monitor key nutritional markers in premature infants. The differences in results compared with a commercially-available nephelometric assay revealed questionable results for lower concentrations by immunoassay.

Establishing evidence-based thresholds and laboratory practices to reduce inappropriate treatment of pseudohyperkalemia.

BACKGROUND: Unrecognized pseudohyperkalemia (PHK), defined as an artificial increase in measured potassium concentration, due to thrombocytosis and leukocytosis can lead to inappropriate patient treatment. Understanding the laboratory and patient characteristics that increase risk of PHK is key to preventing diagnostic errors. METHODS: Serum/plasma potassium results collected at 2 laboratories over 4years were selected based on blood cell counts collected within 24h and whole blood potassium concentrations determined within 2h of the serum/plasma sample. Differences between whole blood and serum or plasma potassium were compared as functions of platelet or leukocyte count, fit to linear models, and stratified based on leukemia diagnosis codes. Patients having a serum/plasma potassium concentration that was at least 1mEq/mL higher than the whole blood concentration were defined as having PHK. Based on this analysis, high-risk patients were prospectively identified and PHK risk was communicated to providers. Medication administration records were queried to compare rates of kayexalate use pre- and post-intervention. RESULTS: Approximately 14% of serum samples with platelet counts >500×109/L had a>1mEq/L increase relative to whole blood potassium. >25% of serum and plasma samples showed a>1mEq/L increase relative to whole blood potassium when leukocyte counts were >50×109/L. Patients with chronic lymphocytic leukemia and high WBC count demonstrated the highest rates of PHK. The rate of kayexalate administration prior to confirmatory testing decreased from 37% to 16% after the laboratory started verbally communicating the possibility of PHK to treating providers. CONCLUSIONS: According to our data, a leukocyte count threshold for plasma samples of 50×109/L is appropriate for indicating a high risk of PHK. Direct communication by the laboratory to the care team reduces inappropriate potassium lowering treatment in populations at high risk.

Laboratory Utilization and Analytical Validation of Fecal Electrolyte Tests.

BACKGROUND: Chronic diarrhea can be categorized as fatty, watery, or inflammatory. Watery diarrhea is further divided into secretory or osmotic types and can be differentiated by measuring fecal electrolytes and osmotic gap. However, with widespread use of endoscopy, it is unclear if these measurements are being used clinically. Furthermore, because stool is not a validated specimen type for Food and Drug Administration-approved electrolyte assays, utilization is a practical concern for laboratories before analytical validation. Here, we determined the clinical utility and validated the performance characteristics of stool electrolytes on the Beckman Coulter AU680. METHODS: Historical results and literature review were used to determine the clinically relevant ranges for stool electrolytes (Na+, Cl-, K+, phosphate, and Mg2+). Additionally, medical chart review was performed (n = 44 patients) on results to evaluate their clinical utility in chronic diarrhea work-up. Linearity, precision, and stability studies were performed on the AU680. Accuracy was evaluated by comparing results to the Roche Cobas 6000 c501. RESULTS: For all cases, stool electrolytes and osmotic gap proved valuable in chronic diarrhea work-up. The imprecision of the assays ranged from 0% to 5.9%. All assays were found to be linear within the instrument's analytical measurement range with appropriate slopes and intercepts. The bias between the AU680 and the Roche c501 ranged from -0.48 to 2.39 (mmol/L or mg/dL). Na+, Cl-, and K+ were stable refrigerated for 5 days and up to 1 freeze-thaw cycle. Phosphate and Mg2+ were stable refrigerated for 48 h, but unstable to freeze-thaw cycles. CONCLUSIONS: Stool osmotic gap is valuable for evaluating chronic diarrhea and can be calculated using electrolyte concentrations measured on the AU680.

Factors influencing naproxen metabolite interference in total bilirubin assays.

BACKGROUND: The factors influencing naproxen metabolite O-desmethylnaproxen (ODMN) positive interference in diazo-based Jendrassik and Grof (JG) total bilirubin (Tbil) assays and lack of interference in direct bilirubin (Dbil) assays have not been resolved. The objective of this study was to understand the conditions causing this interference pattern. METHODS: Pooled normal and ultra-filtered plasma samples spiked with ODMN and naproxen were measured on the Beckman Coulter DxC and AU instruments. Absorbance spectra were obtained for ODMN mixed with Dbil reagent at original and adjusted pH. Absorbance spectra were also obtained for ODMN and bilirubin samples mixed with Tbil assay reagents. RESULTS: ODMN produces a positive interference in the DxC JG Tbil assays, but not the AU Tbil or Dbil assays or the DxC Dbil assay. Neutralizing the acidic pH of AU and DxC Dbil reagents allows ODMN to react with diazo salts. ODMN samples mixed with DxC and AU Tbil reagents produce broad peaks from 450 to 560nm and 400 to 540nm, respectively. The DxC JG Tbil assay monitors a change in absorbance at 520nm close to peak absorbance wavelength of diazo-reacted ODMN, whereas the AU Tbil assay monitors a change in absorbance at 570/660nm, beyond the peak absorbance wavelengths of diazo-reacted ODMN. CONCLUSION: The acidic pH of diazo-based Dbil assay reagents inhibits the reaction of ODMN with diazo salts. The AU JG Tbil assay is a reliable method to measure Tbil in the setting of naproxen overdose.

Endogenous alkaline phosphatase interference in cardiac troponin I and other sensitive chemiluminescence immunoassays that use alkaline phosphatase activity for signal amplification.

BACKGROUND: False positive cardiac troponin results can lead to inappropriate diagnosis. Our laboratory workflow includes systematic quality practices to identify false positive cardiac troponin I (cTnI) results reported by the DxI AccuTnI+3 assay, which uses alkaline phosphatase (ALP) for signal amplification. Recently, a sample with elevated cTnI failed our quality standards and was found to have extremely elevated endogenous ALP activity. The objective of this study was to determine the true cTnI concentration and evaluate whether ALP was the source of interference. METHODS: The suspicious cTnI result was evaluated by repeat analyses, dilution, heterophile blocking treatment, alternative methodology (Vista), and heat treatment. Purified ALP was added to reference serum and we quantified DxI cTnI and human chorionic gonadotropin (hCG). Next, cTnI and/or hCG was measured in specimens with normal (N=20) or elevated (N=26) ALP using DxI and Vista assays. Finally, cTnI was quantified using a prototype, ALP-dependent high-sensitivity assay. RESULTS: The sentinel sample's DxI-cTnI results were imprecise on repeat, linear on dilution, unaffected by heterophile blocking antibodies, and correlated with ALP lability following heat treatment. The Vista-cTnI concentrations were ~7-fold lower. Addition of purified ALP to reference serum linearly increased the DxI-cTnI results. DxI-hCG results also appeared affected by ALP. Several independent patients' specimens with elevated ALP appeared to have falsely elevated DxI-cTnI and DxI-hCG. CONCLUSIONS: Elevated ALP can interfere with contemporary, ALP-dependent immunoassays, including DxI-cTnI and DxI-hCG. The validation of such methods should include evaluations for endogenous ALP interference. Specimens with ALP >1000U/L and elevated DxI-cTnI should be evaluated for ALP interference.

Therapeutic concentrations of hydroxocobalamin interferes with several spectrophotometric assays on the Beckman Coulter DxC and AU680 chemistry analyzers.

BACKGROUND: High doses of hydroxocobalamin (OHCob) are used to treat cyanide poisoning and cardiac complications. Since OHCob absorbs at multiple wavelengths often used in colorimetric assays, spurious laboratory results are likely to occur. The objective of this study was to examine interference caused by OHCob in colorimetric assays measured using the Beckman Coulter DxC and AU680. METHODS: OHCob was dissolved in water and spiked into pooled "healthy" and "unhealthy" patient samples at two different concentrations (0.15 and 1.5 mg/mL). Spiked and unspiked samples were analyzed on both instruments and bias was calculated. A total of 23 analytes were tested on the DxC and 27 analytes were tested on the AU680. For analytes showing a bias ≥ 10%, OHCob was titrated from 0.2-1.5mg/mL. RESULTS: The following analytes were affected on the DxC and AU680: alanine aminotransferase, amylase, total bilirubin, cholesterol, creatine kinase, creatinine, magnesium, uric acid. Direct bilirubin, iron, phosphate, total protein and triglycerides were only affected on the DxC. Biases observed were positive or negative and fixed or proportional. CONCLUSIONS: Between the DxC and AU680, several analytes were affected at therapeutic OHCob concentrations. Hence, it is important for laboratories to know how their instruments are affected, and for clinicians to alert the lab when these samples are expected.

Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src.

Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases.

Affinity purification of protein kinases that adopt a specific inactive conformation.

Several protein kinases have been characterized in a specific inactive form called the DFG-out conformation. Unlike the active conformation which is conserved in all kinases, the inactive DFG-out conformation appears to be accessible to only certain kinases. This inactive conformation has been successfully targeted with highly selective kinase inhibitors, including the cancer drugs imatinib and sorafenib. However, the structural and sequence requirements for adopting this conformation are still poorly understood. Here, we describe a general method for enriching DFG-out adopting kinases from cell lysates with an affinity resin that contains a general ligand that specifically recognizes this inactive form.

Determination of the kinetics and thermodynamics of ligand binding to a specific inactive conformation in protein kinases.

Recent interest in inactive kinase conformations has generated the need to develop new biochemical tools to study them. Here, we describe the use of a fluorescent probe that selectively and potently binds to a specific inactive conformation of protein kinases. This allows for the thermodynamics and kinetics of ligand binding to be determined.

Affinity reagents that target a specific inactive form of protein kinases.

A number of small-molecule inhibitors have been developed that target the catalytic domains of protein kinases that are not in an active conformation. An inactive form that has been observed in several kinases is the DFG-out conformation. This conformation is characterized by an almost 180 degrees rotation of the conserved Asp-Phe-Gly (DFG) motif in the ATP-binding cleft relative to the active form. However, the sequence and structural determinants that allow a kinase to stably adopt the DFG-out conformation are not known. Here, we characterize a series of inhibitors based on a general pharmacophore for this inactive form. We demonstrate that modified versions of these inhibitors can be used to study the thermodynamics and kinetics of ligand binding to DFG-out-adopting kinases and for enriching these kinases from complex protein mixtures.

Reactive landing of gas-phase ions as a tool for the fabrication of metal oxide surfaces for in situ phosphopeptide enrichment.

Zirconium, titanium, and hafnium oxide-coated stainless steel surfaces are fabricated by reactive landing of gas-phase ions produced by electrospray ionization of group IVB metal alkoxides. The surfaces are used for in situ enrichment of phosphopeptides before analysis by matrix-assisted laser desorption ionization (MALDI) mass spectrometry. To evaluate this method we characterized ZrO(2) (zirconia) surfaces by (1) comparison with the other group IVB metal oxides of TiO(2) (titania) and HfO(2) (hafnia), (2) morphological characterization by SEM image analysis, and (3) dependence of phosphopeptide enrichment on the metal oxide layer thickness. Furthermore, we evaluated the necessity of the reactive landing process for the construction of useful metal oxide surfaces by preparing surfaces by electrospray deposition of Zr, Ti, and Hf alkoxides directly onto polished metal surfaces at atmospheric pressure. Although all three metal oxide surfaces evaluated were capable of phosphopeptide enrichment from complex peptide mixtures, zirconia performed better than hafnia or titania as a result of morphological characteristics illustrated by the SEM analysis. Metal oxide coatings that were fabricated by atmospheric pressure deposition were still capable of in situ phosphopeptide enrichment, although with inferior efficiency and surface durability. We show that zirconia surfaces prepared by reactive landing of gas-phase ions can be a useful tool for high throughput screening of novel phosphorylation sites and quantitation of phosphorylation kinetics.

Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations.

Imatinib is an inhibitor of the Abl tyrosine kinase domain that is effective in the treatment of chronic myelogenic leukemia. Although imatinib binds tightly to the Abl kinase domain, its affinity for the closely related kinase domain of c-Src is at least 2,000-fold lower. Imatinib recognition requires a specific inactive conformation of the kinase domain, in which a conserved Asp-Phe-Gly (DFG) motif is flipped with respect to the active conformation. The inability of c-Src to readily adopt this flipped DFG conformation was thought to underlie the selectivity of imatinib for Abl over c-Src. Here, we present a series of inhibitors (DSA compounds) that are based on the core scaffold of imatinib but which bind with equally high potency to c-Src and Abl. The DSA compounds bind to c-Src in the DFG-flipped conformation, as confirmed by crystal structures and kinetic analysis. The origin of the high affinity of these compounds for c-Src is suggested by the fact that they also inhibit clinically relevant Abl variants bearing mutations in a structural element, the P-loop, that normally interacts with the phosphate groups of ATP but is folded over a substructure of imatinib in Abl. Importantly, several of the DSA compounds block the growth of Ba/F3 cells harboring imatinib-resistant BCR-ABL mutants, including the Thr315Ile "gatekeeper" mutation, but do not suppress the growth of parental Ba/F3 cells.