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Phipps WS, Greene DN, Pflaum H, Laha TJ, Dickerson JA, Irvine J, Merrill AE, Ranjitkar P, Henderson CM, Hoofnagle AN. Small volume retinol binding protein measurement by liquid chromatography-tandem mass spectrometry. Clin Biochem 2022; 99:111-117. [PMID: 34678307 PMCID: PMC8671195 DOI: 10.1016/j.clinbiochem.2021.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/13/2021] [Accepted: 10/17/2021] [Indexed: 01/03/2023]
Abstract
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.
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Affiliation(s)
- William S. Phipps
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Dina N. Greene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Hannah Pflaum
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Thomas J. Laha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Jane A. Dickerson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA,Seattle Children’s Hospital, Seattle, WA
| | - Jill Irvine
- University of Washington Medical Center, Seattle, WA
| | - Anna E. Merrill
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Pratistha Ranjitkar
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Clark M. Henderson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Andrew N. Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA,Department of Medicine, University of Washington, Seattle, WA
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Ronen S, Ranjitkar P, Colón-Franco J. 28 Interference of Over-the-Counter Administration of Biotin on Elecsys Roche Immunoassays. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqx115.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Carrillo L, Monzel D, Ranjitkar P, Colon-Franco J. 31 Utility of Epinephrine in Determining Accurate Catheterization in Adrenal Vein Sampling Procedures. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqx149.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Hopp AM, Ranjitkar P, Colon-Franco JM. Unexpected Change in Thyroglobulin Concentration. Clin Chem 2017; 63:1775. [PMID: 29089325 DOI: 10.1373/clinchem.2017.274639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/18/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Amanda M Hopp
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI.
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Parakh R, Greene DN, Mathias PC, Block DR, Ranjitkar P. Laboratory Utilization and Analytical Validation of Fecal Electrolyte Tests. J Appl Lab Med 2017; 1:668-677. [PMID: 33379818 DOI: 10.1373/jalm.2016.022590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/09/2017] [Indexed: 11/06/2022]
Abstract
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.
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Affiliation(s)
- Rugvedita Parakh
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Department of Pathology, University of Washington, Seattle, WA
| | - Dina N Greene
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Patrick C Mathias
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Darci R Block
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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Ranjitkar P, Greene D, Mathias P. Effective Laboratory Communication Reduces Inappropriate Treatment of Pseudohyperkalemia. Am J Clin Pathol 2017. [DOI: 10.1093/ajcp/aqw191.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ranjitkar P, Turtle CJ, Harris NS, Holmes DT, Pyle-Eilola A, Maloney DG, Greene DN. Susceptibility of commonly used ferritin assays to the classic hook effect. Clin Chem Lab Med 2016; 54:e41-3. [PMID: 26351953 DOI: 10.1515/cclm-2015-0604] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/15/2015] [Indexed: 11/15/2022]
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Ranjitkar P, Greene DN. Therapeutic concentrations of hydroxocobalamin interferes with several spectrophotometric assays on the Beckman Coulter DxC and AU680 chemistry analyzers. Clin Chim Acta 2015; 450:110-4. [DOI: 10.1016/j.cca.2015.07.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/17/2015] [Accepted: 07/25/2015] [Indexed: 10/23/2022]
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Ranjitkar P, Harris NS, Holmes DT, Pyle-Eilola A, Turtle CJ, Greene DN. 67: Susceptibility of Commonly Used Ferritin Assays to the Classic Hook Effect. Am J Clin Pathol 2015. [DOI: 10.1093/ajcp/143.suppl1.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Neil S. Harris
- Department of Pathology, University of Florida, Gainesville
| | | | | | - Cameron J. Turtle
- Department of Laboratory Medicine, University of Washington, Seattle
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Dina N. Greene
- Department of Laboratory Medicine, University of Washington, Seattle
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Saifee NH, Ranjitkar P, Greene DN. 40: Spectral Wavelength and pH: A Mechanism for Naproxen Metabolite Positive Interference in Total Bilirubin Assays. Am J Clin Pathol 2015. [DOI: 10.1093/ajcp/143.suppl1.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nabiha Huq Saifee
- Department of Laboratory Medicine, University of Washington, Seattle
| | | | - Dina N. Greene
- Department of Laboratory Medicine, University of Washington, Seattle
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Hari SB, Perera BGK, Ranjitkar P, Seeliger MA, Maly DJ. Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src. ACS Chem Biol 2013; 8:2734-43. [PMID: 24106839 DOI: 10.1021/cb400663k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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.
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Affiliation(s)
- Sanjay B. Hari
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - B. Gayani K. Perera
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Pratistha Ranjitkar
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York 11794, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Ranjitkar P, Perera BGK, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ. Correction to “Affinity-Based Probes Based on Type II Kinase Inhibitors”. J Am Chem Soc 2013. [DOI: 10.1021/ja3120967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Krishnamurty R, Brigham JL, Leonard SE, Ranjitkar P, Larson ET, Dale EJ, Merritt EA, Maly DJ. Active site profiling reveals coupling between domains in SRC-family kinases. Nat Chem Biol 2012; 9:43-50. [PMID: 23143416 PMCID: PMC3522794 DOI: 10.1038/nchembio.1118] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 10/01/2012] [Indexed: 12/14/2022]
Abstract
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 for 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 display a distinct preference for autoinhibited forms of these kinases. Furthermore, we show that ligands that demonstrate 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.
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Ranjitkar P, Perera BGK, Swaney DL, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ. Affinity-based probes based on type II kinase inhibitors. J Am Chem Soc 2012; 134:19017-25. [PMID: 23088519 DOI: 10.1021/ja306035v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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.
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Affiliation(s)
- Pratistha Ranjitkar
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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Andrews S, Perera G, Ranjitkar P, Maly D. Label Transfer Reagents for the Study of Protein Kinase Complexes. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.755.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Dustin Maly
- Dept. of ChemistryUniversity of WashingtonSeattleWA
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Hari SB, Ranjitkar P, Maly DJ. Determination of the kinetics and thermodynamics of ligand binding to a specific inactive conformation in protein kinases. Methods Mol Biol 2012; 928:153-9. [PMID: 22956140 PMCID: PMC5228460 DOI: 10.1007/978-1-62703-008-3_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
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.
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Affiliation(s)
- Sanjay B. Hari
- Correspondence: Sanjay B. Hari, Department of Chemistry, Box 351700, Seattle, WA 98195, USA. Tel: (206) 616-4269;
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Ranjitkar P, Brock AM, Maly DJ. Affinity reagents that target a specific inactive form of protein kinases. ACTA ACUST UNITED AC 2010; 17:195-206. [PMID: 20189109 DOI: 10.1016/j.chembiol.2010.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/18/2010] [Accepted: 01/20/2010] [Indexed: 02/01/2023]
Abstract
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.
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Blacken GR, Volný M, Diener M, Jackson KE, Ranjitkar P, Maly DJ, Turecek F. Reactive landing of gas-phase ions as a tool for the fabrication of metal oxide surfaces for in situ phosphopeptide enrichment. J Am Soc Mass Spectrom 2009; 20:915-926. [PMID: 19251440 DOI: 10.1016/j.jasms.2009.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 01/11/2009] [Accepted: 01/13/2009] [Indexed: 05/27/2023]
Abstract
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.
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Affiliation(s)
- Grady R Blacken
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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Seeliger MA, Ranjitkar P, Kasap C, Shan Y, Shaw DE, Shah NP, Kuriyan J, Maly DJ. Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations. Cancer Res 2009; 69:2384-92. [PMID: 19276351 DOI: 10.1158/0008-5472.can-08-3953] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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.
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Affiliation(s)
- Markus A Seeliger
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkely, USA
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