1
|
de Campos CB, Zhu YX, Sepetov N, Romanov S, Bruins LA, Shi CX, Stein CK, Petit JL, Polito AN, Sharik ME, Meermeier EW, Ahmann GJ, Armenta IDL, Kruse J, Bergsagel PL, Chesi M, Meurice N, Braggio E, Stewart AK. Identification of PIKfyve kinase as a target in multiple myeloma. Haematologica 2019; 105:1641-1649. [PMID: 31582538 PMCID: PMC7271606 DOI: 10.3324/haematol.2019.222729] [Citation(s) in RCA: 21] [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: 03/21/2019] [Accepted: 09/26/2019] [Indexed: 01/03/2023] Open
Abstract
The cellular cytotoxicity of APY0201, a PIKfyve inhibitor, against multiple myeloma was initially identified in an unbiased in vitro chemical library screen. The activity of APY0201 was confirmed in all 25 cell lines tested and in 40% of 100 ex vivo patient-derived primary samples, with increased activity in primary samples harboring trisomies and lacking t(11;14). The broad anti-multiple myeloma activity of PIKfyve inhibitors was further demonstrated in confirmatory screens and showed the superior potency of APY0201 when compared to the PIKfyve inhibitors YM201636 and apilimod, with a mid-point half maximal effective concentration (EC50) at nanomolar concentrations in, respectively, 65%, 40%, and 5% of the tested cell lines. Upregulation of genes in the lysosomal pathway and increased cellular vacuolization were observed in vitro following APY0201 treatment, although these cellular effects did not correlate well with responsiveness. We confirm that PIKfyve inhibition is associated with activation of the transcription factor EB, a master regulator of lysosomal biogenesis and autophagy. Furthermore, we established an assay measuring autophagy as a predictive marker of APY0201 sensitivity. Overall, these findings indicate promising activity of PIKfyve inhibitors secondary to disruption of autophagy in multiple myeloma and suggest a strategy to enrich for likely responders.
Collapse
Affiliation(s)
| | - Yuan Xiao Zhu
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | | | | | - Laura Ann Bruins
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Chang-Xin Shi
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Caleb K Stein
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Joachim L Petit
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Alysia N Polito
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Meaghen E Sharik
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Erin W Meermeier
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Gregory J Ahmann
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | | | - Jonas Kruse
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - P Leif Bergsagel
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Marta Chesi
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Nathalie Meurice
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - Esteban Braggio
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| | - A Keith Stewart
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ
| |
Collapse
|
2
|
Elkins JM, Fedele V, Szklarz M, Abdul Azeez KR, Salah E, Mikolajczyk J, Romanov S, Sepetov N, Huang XP, Roth BL, Al Haj Zen A, Fourches D, Muratov E, Tropsha A, Morris J, Teicher BA, Kunkel M, Polley E, Lackey KE, Atkinson FL, Overington JP, Bamborough P, Müller S, Price DJ, Willson TM, Drewry DH, Knapp S, Zuercher WJ. Comprehensive characterization of the Published Kinase Inhibitor Set. Nat Biotechnol 2015; 34:95-103. [PMID: 26501955 DOI: 10.1038/nbt.3374] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 08/31/2015] [Indexed: 12/21/2022]
Abstract
Despite the success of protein kinase inhibitors as approved therapeutics, drug discovery has focused on a small subset of kinase targets. Here we provide a thorough characterization of the Published Kinase Inhibitor Set (PKIS), a set of 367 small-molecule ATP-competitive kinase inhibitors that was recently made freely available with the aim of expanding research in this field and as an experiment in open-source target validation. We screen the set in activity assays with 224 recombinant kinases and 24 G protein-coupled receptors and in cellular assays of cancer cell proliferation and angiogenesis. We identify chemical starting points for designing new chemical probes of orphan kinases and illustrate the utility of these leads by developing a selective inhibitor for the previously untargeted kinases LOK and SLK. Our cellular screens reveal compounds that modulate cancer cell growth and angiogenesis in vitro. These reagents and associated data illustrate an efficient way forward to increasing understanding of the historically untargeted kinome.
Collapse
Affiliation(s)
- Jonathan M Elkins
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Vita Fedele
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Marta Szklarz
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Kamal R Abdul Azeez
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | | | | | | | - Xi-Ping Huang
- The National Institute of Mental Health Psychoactive Active Drug Screening Program, (NIMH PDSP), Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, The University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Bryan L Roth
- The National Institute of Mental Health Psychoactive Active Drug Screening Program, (NIMH PDSP), Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, The University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Ayman Al Haj Zen
- British Heart Foundation Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Denis Fourches
- Laboratory for Molecular Modeling Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eugene Muratov
- Laboratory for Molecular Modeling Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alex Tropsha
- Laboratory for Molecular Modeling Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel Morris
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | - Beverly A Teicher
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | - Mark Kunkel
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | - Eric Polley
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | - Karen E Lackey
- Medical University of South Carolina, Charleston, South Carolina, USA
| | - Francis L Atkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - John P Overington
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Susanne Müller
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Daniel J Price
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - Timothy M Willson
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - David H Drewry
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - Stefan Knapp
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK.,Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - William J Zuercher
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| |
Collapse
|
3
|
Popa-Burke IG, Issakova O, Arroway JD, Bernasconi P, Chen M, Coudurier L, Galasinski S, Jadhav AP, Janzen WP, Lagasca D, Liu D, Lewis RS, Mohney RP, Sepetov N, Sparkman DA, Hodge CN. Streamlined System for Purifying and Quantifying a Diverse Library of Compounds and the Effect of Compound Concentration Measurements on the Accurate Interpretation of Biological Assay Results. Anal Chem 2004; 76:7278-87. [PMID: 15595870 DOI: 10.1021/ac0491859] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As part of an overall systems approach to generating highly accurate screening data across large numbers of compounds and biological targets, we have developed and implemented streamlined methods for purifying and quantitating compounds at various stages of the screening process, coupled with automated "traditional" storage methods (DMSO, -20 degrees C). Specifically, all of the compounds in our druglike library are purified by LC/MS/UV and are then controlled for identity and concentration in their respective DMSO stock solutions by chemiluminescent nitrogen detection (CLND)/evaporative light scattering detection (ELSD) and MS/UV. In addition, the compound-buffer solutions used in the various biological assays are quantitated by LC/UV/CLND to determine the concentration of compound actually present during screening. Our results show that LC/UV/CLND/ELSD/MS is a widely applicable method that can be used to purify, quantitate, and identify most small organic molecules from compound libraries. The LC/UV/CLND technique is a simple and sensitive method that can be easily and cost-effectively employed to rapidly determine the concentrations of even small amounts of any N-containing compound in aqueous solution. We present data to establish error limits for concentration determination that are well within the overall variability of the screening process. This study demonstrates that there is a significant difference between the predicted amount of soluble compound from stock DMSO solutions following dilution into assay buffer and the actual amount present in assay buffer solutions, even at the low concentrations employed for the assays. We also demonstrate that knowledge of the concentrations of compounds to which the biological target is exposed is critical for accurate potency determinations. Accurate potency values are in turn particularly important for drug discovery, for understanding structure-activity relationships, and for building useful empirical models of protein-ligand interactions. Our new understanding of relative solubility demonstrates that most, if not all, decisions that are made in early discovery are based upon missing or inaccurate information. Finally, we demonstrate that careful control of compound handling and concentration, coupled with accurate assay methods, allows the use of both positive and negative data in analyzing screening data sets for structure-activity relationships that determine potency and selectivity.
Collapse
Affiliation(s)
- Ioana G Popa-Burke
- Amphora Discovery Corporation, P.O. Box 12169, Research Triangle Park, North Carolina 27709, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Ostrem JA, al-Obeidi F, Safar P, Safarova A, Stringer SK, Patek M, Cross MT, Spoonamore J, LoCascio JC, Kasireddy P, Thorpe DS, Sepetov N, Lebl M, Wildgoose P, Strop P. Discovery of a novel, potent, and specific family of factor Xa inhibitors via combinatorial chemistry. Biochemistry 1998; 37:1053-9. [PMID: 9454596 DOI: 10.1021/bi971147e] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A series of low molecular weight peptide inhibitors of factor Xa, unrelated to any previously described, was identified by screening a combinatorial peptide library composed of L-amino acids. The minimal inhibitory sequence is a tripeptide, L-tyrosinyl-L-isoleucyl-L-arginyl, which competitively inhibits the hydrolysis of small chromogenic substrates by factor Xa but binds in an orientation which prevents a productive nucleophilic attack by serine 195 of the catalytic triad on the carbonyl carbon of the carboxyterminal arginine. The initial leads identified in an octamer combinatorial peptide library ranged in potency from 4 to 15 microM. These peptides were modified into peptide mimetics with a greater than 1000-fold increase in potency while retaining unusual selectivity for factor Xa over the related serine proteases thrombin, factor VIIa/tissue factor, plasmin, activated protein C, kallikrein, and trypsin. One of the most potent analogues, SEL 2711, with a Ki of 0.003 microM for factor Xa and 40 microM for thrombin, is active in in vitro and ex vivo coagulation assays, suggesting the potential application of these inhibitors in anticoagulant therapy.
Collapse
Affiliation(s)
- J A Ostrem
- Selectide Corporation, Tucson, Arizona 85737, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|