1
|
Kailass K, Casalena D, Jenane L, McEdwards G, Auld DS, Sadovski O, Kaye EG, Hudson E, Nettleton D, Currie MA, Beharry AA. Tight-Binding Small-Molecule Carboxylesterase 2 Inhibitors Reduce Intracellular Irinotecan Activation. J Med Chem 2024; 67:2019-2030. [PMID: 38265364 DOI: 10.1021/acs.jmedchem.3c01850] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 01/25/2024]
Abstract
As the primary enzyme responsible for the activatable conversion of Irinotecan (CPT-11) to SN-38, carboxylesterase 2 (CES2) is a significant predictive biomarker toward CPT-11-based treatments for pancreatic ductal adenocarcinoma (PDAC). High SN-38 levels from high CES2 activity lead to harmful effects, including life-threatening diarrhea. While alternate strategies have been explored, CES2 inhibition presents an effective strategy to directly alter the pharmacokinetics of CPT-11 conversion, ultimately controlling the amount of SN-38 produced. To address this, we conducted a high-throughput screening to discover 18 small-molecule CES2 inhibitors. The inhibitors are validated by dose-response and counter-screening and 16 of these inhibitors demonstrate selectivity for CES2. These 16 inhibitors inhibit CES2 in cells, indicating cell permeability, and they show inhibition of CPT-11 conversion with the purified enzyme. The top five inhibitors prohibited cell death mediated by CPT-11 when preincubated in PDAC cells. Three of these inhibitors displayed a tight-binding mechanism of action with a strong binding affinity.
Collapse
Affiliation(s)
- Karishma Kailass
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Dominick Casalena
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Lina Jenane
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Gregor McEdwards
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada, L5L 1C6
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Oleg Sadovski
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Esther G Kaye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Elyse Hudson
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - David Nettleton
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Mark A Currie
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada, L5L 1C6
| | - Andrew A Beharry
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
| |
Collapse
|
2
|
Abbott KL, Ali A, Casalena D, Do BT, Ferreira R, Cheah JH, Soule CK, Deik A, Kunchok T, Schmidt DR, Renner S, Honeder SE, Wu M, Chan SH, Tseyang T, Stoltzfus AT, Michel SLJ, Greaves D, Hsu PP, Ng CW, Zhang CJ, Farsidjani A, Kent JR, Madariaga MLL, Gramatikov IMT, Matheson NJ, Lewis CA, Clish CB, Rees MG, Roth JA, Griner LM, Muir A, Auld DS, Vander Heiden MG. Screening in serum-derived medium reveals differential response to compounds targeting metabolism. Cell Chem Biol 2023; 30:1156-1168.e7. [PMID: 37689063 PMCID: PMC10581593 DOI: 10.1016/j.chembiol.2023.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 09/11/2023]
Abstract
A challenge for screening new anticancer drugs is that efficacy in cell culture models is not always predictive of efficacy in patients. One limitation of standard cell culture is a reliance on non-physiological nutrient levels, which can influence cell metabolism and drug sensitivity. A general assessment of how physiological nutrients affect cancer cell response to small molecule therapies is lacking. To address this, we developed a serum-derived culture medium that supports the proliferation of diverse cancer cell lines and is amenable to high-throughput screening. We screened several small molecule libraries and found that compounds targeting metabolic enzymes were differentially effective in standard compared to serum-derived medium. We exploited the differences in nutrient levels between each medium to understand why medium conditions affected the response of cells to some compounds, illustrating how this approach can be used to screen potential therapeutics and understand how their efficacy is modified by available nutrients.
Collapse
Affiliation(s)
- Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmed Ali
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dominick Casalena
- Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Raphael Ferreira
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jaime H Cheah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christian K Soule
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Daniel R Schmidt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Steffen Renner
- Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Sophie E Honeder
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Michelle Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Tenzin Tseyang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Andrew T Stoltzfus
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Daniel Greaves
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Peggy P Hsu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02113, USA
| | - Christopher W Ng
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chelsea J Zhang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ali Farsidjani
- Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Johnathan R Kent
- Department of Surgery, University of Chicago Medicine, Chicago, IL 60637, USA
| | | | - Iva Monique T Gramatikov
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Nicholas J Matheson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew G Rees
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Alexander Muir
- Ben May Department of Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Douglas S Auld
- Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA.
| |
Collapse
|
3
|
Abbott KL, Ali A, Casalena D, Do BT, Ferreira R, Cheah JH, Soule CK, Deik A, Kunchok T, Schmidt DR, Renner S, Honeder SE, Wu M, Chan SH, Tseyang T, Greaves D, Hsu PP, Ng CW, Zhang CJ, Farsidjani A, Gramatikov IMT, Matheson NJ, Lewis CA, Clish CB, Rees MG, Roth JA, Griner LM, Muir A, Auld DS, Heiden MGV. Screening in serum-derived medium reveals differential response to compounds targeting metabolism. bioRxiv 2023:2023.02.25.529972. [PMID: 36909640 PMCID: PMC10002634 DOI: 10.1101/2023.02.25.529972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
A challenge for screening new candidate drugs to treat cancer is that efficacy in cell culture models is not always predictive of efficacy in patients. One limitation of standard cell culture is a reliance on non-physiological nutrient levels to propagate cells. Which nutrients are available can influence how cancer cells use metabolism to proliferate and impact sensitivity to some drugs, but a general assessment of how physiological nutrients affect cancer cell response to small molecule therapies is lacking. To enable screening of compounds to determine how the nutrient environment impacts drug efficacy, we developed a serum-derived culture medium that supports the proliferation of diverse cancer cell lines and is amenable to high-throughput screening. We used this system to screen several small molecule libraries and found that compounds targeting metabolic enzymes were enriched as having differential efficacy in standard compared to serum-derived medium. We exploited the differences in nutrient levels between each medium to understand why medium conditions affected the response of cells to some compounds, illustrating how this approach can be used to screen potential therapeutics and understand how their efficacy is modified by available nutrients.
Collapse
Affiliation(s)
- Keene L. Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmed Ali
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dominick Casalena
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Brian T. Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA
| | | | - Jaime H. Cheah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christian K. Soule
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Daniel R. Schmidt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Steffen Renner
- Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Sophie E. Honeder
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Michelle Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Tenzin Tseyang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Daniel Greaves
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Peggy P. Hsu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Massachusetts General Hospital Cancer Center, Boston, MA 02113, USA
| | - Christopher W. Ng
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chelsea J. Zhang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ali Farsidjani
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Iva Monique T. Gramatikov
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicholas J. Matheson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Caroline A. Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew G. Rees
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Lesley Mathews Griner
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Alexander Muir
- Ben May Department of Cancer Research, University of Chicago, Chicago, IL, USA
| | - Douglas S. Auld
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Matthew G. Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Dana-Farber Cancer Institute, Boston, MA 02115, USA
| |
Collapse
|
4
|
Coussens NP, Auld DS, Thielman JR, Wagner BK, Dahlin JL. Addressing Compound Reactivity and Aggregation Assay Interferences: Case Studies of Biochemical High-Throughput Screening Campaigns Benefiting from the National Institutes of Health Assay Guidance Manual Guidelines. SLAS Discov 2021; 26:1280-1290. [PMID: 34218710 DOI: 10.1177/24725552211026239] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Compound-dependent assay interferences represent a continued burden in drug and chemical probe discovery. The open-source National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS) Assay Guidance Manual (AGM) established an "Assay Artifacts and Interferences" section to address different sources of artifacts and interferences in biological assays. In addition to the frequent introduction of new chapters in this important topic area, older chapters are periodically updated by experts from academia, industry, and government to include new technologies and practices. Section chapters describe many best practices for mitigating and identifying compound-dependent assay interferences. Using two previously reported biochemical high-throughput screening campaigns for small-molecule inhibitors of the epigenetic targets Rtt109 and NSD2, the authors review best practices and direct readers to high-yield resources in the AGM and elsewhere for the mitigation and identification of compound-dependent reactivity and aggregation assay interferences.
Collapse
Affiliation(s)
- Nathan P Coussens
- Molecular Pharmacology Laboratories, Division of Cancer Treatment and Diagnosis Laboratory Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| |
Collapse
|
5
|
Khan SA, Park KM, Fischer LA, Dong C, Lungjangwa T, Jimenez M, Casalena D, Chew B, Dietmann S, Auld DS, Jaenisch R, Theunissen TW. Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening. Cell Rep 2021; 35:109233. [PMID: 34133938 PMCID: PMC8272458 DOI: 10.1016/j.celrep.2021.109233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/25/2021] [Accepted: 05/19/2021] [Indexed: 01/04/2023] Open
Abstract
Naive human embryonic stem cells (hESCs) have been isolated that more closely resemble the pre-implantation epiblast compared to conventional “primed” hESCs, but the signaling principles underlying these discrete stem cell states remain incompletely understood. Here, we describe the results from a high-throughput screen using ~3,000 well-annotated compounds to identify essential signaling requirements for naive human pluripotency. We report that MEK1/2 inhibitors can be replaced during maintenance of naive human pluripotency by inhibitors targeting either upstream (FGFR, RAF) or downstream (ERK1/2) kinases. Naive hESCs maintained under these alternative conditions display elevated levels of ERK phosphorylation but retain genome-wide DNA hypomethylation and a transcriptional identity of the pre-implantation epiblast. In contrast, dual inhibition of MEK and ERK promotes efficient primed-to-naive resetting in combination with PKC, ROCK, and TNKS inhibitors and activin A. This work demonstrates that induction and maintenance of naive human pluripotency are governed by distinct signaling requirements. Khan et al. describe a high-throughput chemical screen to identify essential signaling requirements for naive human pluripotency in minimal conditions. They report that naive hESCs can be maintained by blocking distinct nodes in the FGF signaling pathway and that dual MEK/ERK inhibition promotes efficient primed-to-naive resetting in combination with activin A.
Collapse
Affiliation(s)
- Shafqat A Khan
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kyoung-Mi Park
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A Fischer
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chen Dong
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tenzin Lungjangwa
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Marta Jimenez
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Dominick Casalena
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Brian Chew
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sabine Dietmann
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
6
|
Tan C, Ginzberg MB, Webster R, Iyengar S, Liu S, Papadopoli D, Concannon J, Wang Y, Auld DS, Jenkins JL, Rost H, Topisirovic I, Hilfinger A, Derry WB, Patel N, Kafri R. Cell size homeostasis is maintained by CDK4-dependent activation of p38 MAPK. Dev Cell 2021; 56:1756-1769.e7. [PMID: 34022133 DOI: 10.1016/j.devcel.2021.04.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 07/26/2020] [Revised: 02/08/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
While molecules that promote the growth of animal cells have been identified, it remains unclear how such signals are orchestrated to determine a characteristic target size for different cell types. It is increasingly clear that cell size is determined by size checkpoints-mechanisms that restrict the cell cycle progression of cells that are smaller than their target size. Previously, we described a p38 MAPK-dependent cell size checkpoint mechanism whereby p38 is selectively activated and prevents cell cycle progression in cells that are smaller than a given target size. In this study, we show that the specific target size required for inactivation of p38 and transition through the cell cycle is determined by CDK4 activity. Our data suggest a model whereby p38 and CDK4 cooperate analogously to the function of a thermostat: while p38 senses irregularities in size, CDK4 corresponds to the thermostat dial that sets the target size.
Collapse
Affiliation(s)
- Ceryl Tan
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam B Ginzberg
- Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Rachel Webster
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Seshu Iyengar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, ON L5L 1C6, Canada
| | - Shixuan Liu
- Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - David Papadopoli
- Gerald Bronfman Department of Oncology and Lady Davis Institute, McGill University Montreal, QC H4A 3T2, Canada
| | - John Concannon
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Douglas S Auld
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Hannes Rost
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology and Lady Davis Institute, McGill University Montreal, QC H4A 3T2, Canada
| | - Andreas Hilfinger
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, ON L5L 1C6, Canada
| | - W Brent Derry
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nish Patel
- Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ran Kafri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
| |
Collapse
|
7
|
Dahlin JL, Auld DS, Rothenaigner I, Haney S, Sexton JZ, Nissink JWM, Walsh J, Lee JA, Strelow JM, Willard FS, Ferrins L, Baell JB, Walters MA, Hua BK, Hadian K, Wagner BK. Nuisance compounds in cellular assays. Cell Chem Biol 2021; 28:356-370. [PMID: 33592188 PMCID: PMC7979533 DOI: 10.1016/j.chembiol.2021.01.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/02/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022]
Abstract
Compounds that exhibit assay interference or undesirable mechanisms of bioactivity ("nuisance compounds") are routinely encountered in cellular assays, including phenotypic and high-content screening assays. Much is known regarding compound-dependent assay interferences in cell-free assays. However, despite the essential role of cellular assays in chemical biology and drug discovery, there is considerably less known about nuisance compounds in more complex cell-based assays. In our view, a major obstacle to realizing the full potential of chemical biology will not just be difficult-to-drug targets or even the sheer number of targets, but rather nuisance compounds, due to their ability to waste significant resources and erode scientific trust. In this review, we summarize our collective academic, government, and industry experiences regarding cellular nuisance compounds. We describe assay design strategies to mitigate the impact of nuisance compounds and suggest best practices to efficiently address these compounds in complex biological settings.
Collapse
Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ina Rothenaigner
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Steve Haney
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jarrod Walsh
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park SK10 4TG, UK
| | | | | | | | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02140, USA
| | - Kamyar Hadian
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA
| |
Collapse
|
8
|
Busby SA, Carbonneau S, Concannon J, Dumelin CE, Lee Y, Numao S, Renaud N, Smith TM, Auld DS. Advancements in Assay Technologies and Strategies to Enable Drug Discovery. ACS Chem Biol 2020; 15:2636-2648. [PMID: 32880443 DOI: 10.1021/acschembio.0c00495] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Assays drive drug discovery from the exploratory phases to the clinical testing of drug candidates. As such, numerous assay technologies and methodologies have arisen to support drug discovery efforts. Robust identification and characterization of tractable chemical matter requires biochemical, biophysical, and cellular approaches and often benefits from high-throughput methods. To increase throughput, efforts have been made to provide assays in miniaturized volumes which can be arrayed in microtiter plates to support the testing of as many as 100,000 samples/day. Alongside these efforts has been the growth of microtiter plate-free formats with encoded libraries that can support the screening of billions of compounds, a hunt for new drug modalities, as well as emphasis on more disease relevant formats using complex cell models of disease states. This review will focus on recent developments in high-throughput assay technologies applied to identify starting points for drug discovery. We also provide recommendations on strategies for implementing various assay types to select high quality leads for drug development.
Collapse
Affiliation(s)
- Scott A. Busby
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Seth Carbonneau
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - John Concannon
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | | | - YounKyoung Lee
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Shin Numao
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nicole Renaud
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Thomas M. Smith
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Douglas S. Auld
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| |
Collapse
|
9
|
Reidenbach AG, Mesleh MF, Casalena D, Vallabh SM, Dahlin JL, Leed AJ, Chan AI, Usanov DL, Yehl JB, Lemke CT, Campbell AJ, Shah RN, Shrestha OK, Sacher JR, Rangel VL, Moroco JA, Sathappa M, Nonato MC, Nguyen KT, Wright SK, Liu DR, Wagner FF, Kaushik VK, Auld DS, Schreiber SL, Minikel EV. Multimodal small-molecule screening for human prion protein binders. J Biol Chem 2020; 295:13516-13531. [PMID: 32723867 PMCID: PMC7521658 DOI: 10.1074/jbc.ra120.014905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including 19F-observed and saturation transfer difference (STD) NMR spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection, and in silico screening. A single benzimidazole compound was confirmed in concentration-response, but affinity was very weak (Kd > 1 mm), and it could not be advanced further. The exceptionally low hit rate observed here suggests that PrP is a difficult target for small-molecule binders. Whereas orthogonal binder discovery methods could yield high-affinity compounds, non-small-molecule modalities may offer independent paths forward against prion disease.
Collapse
Affiliation(s)
- Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dominick Casalena
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Sonia M Vallabh
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Prion Alliance, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Jayme L Dahlin
- Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alison J Leed
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alix I Chan
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dmitry L Usanov
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jenna B Yehl
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christopher T Lemke
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Arthur J Campbell
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rishi N Shah
- Undergraduate Research Opportunities Program (UROP), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Om K Shrestha
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Joshua R Sacher
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Victor L Rangel
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jamie A Moroco
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Murugappan Sathappa
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Maria Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Kong T Nguyen
- Artificial Intelligence Molecular Screen (AIMS) Awards Program, Atomwise, San Francisco, California, USA
| | - S Kirk Wright
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - David R Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Florence F Wagner
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Virendar K Kaushik
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Douglas S Auld
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Eric Vallabh Minikel
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Prion Alliance, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
10
|
Canham SM, Wang Y, Cornett A, Auld DS, Baeschlin DK, Patoor M, Skaanderup PR, Honda A, Llamas L, Wendel G, Mapa FA, Aspesi P, Labbé-Giguère N, Gamber GG, Palacios DS, Schuffenhauer A, Deng Z, Nigsch F, Frederiksen M, Bushell SM, Rothman D, Jain RK, Hemmerle H, Briner K, Porter JA, Tallarico JA, Jenkins JL. Systematic Chemogenetic Library Assembly. Cell Chem Biol 2020; 27:1124-1129. [PMID: 32707038 DOI: 10.1016/j.chembiol.2020.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 03/31/2020] [Revised: 06/03/2020] [Accepted: 07/02/2020] [Indexed: 12/22/2022]
Abstract
Chemogenetic libraries, collections of well-defined chemical probes, provide tremendous value to biomedical research but require substantial effort to ensure diversity as well as quality of the contents. We have assembled a chemogenetic library by data mining and crowdsourcing institutional expertise. We are sharing our approach, lessons learned, and disclosing our current collection of 4,185 compounds with their primary annotated gene targets (https://github.com/Novartis/MoaBox). This physical collection is regularly updated and used broadly both within Novartis and in collaboration with external partners.
Collapse
Affiliation(s)
- Stephen M Canham
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Yuan Wang
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Allen Cornett
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Douglas S Auld
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Daniel K Baeschlin
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Maude Patoor
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Philip R Skaanderup
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Ayako Honda
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Luis Llamas
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Greg Wendel
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Felipa A Mapa
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Peter Aspesi
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nancy Labbé-Giguère
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gabriel G Gamber
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Daniel S Palacios
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ansgar Schuffenhauer
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Zhan Deng
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Florian Nigsch
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Mathias Frederiksen
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Simon M Bushell
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Deborah Rothman
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rishi K Jain
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Horst Hemmerle
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Karin Briner
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jeffery A Porter
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jeremy L Jenkins
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| |
Collapse
|
11
|
Griner LM, Gampa K, Do T, Nguyen H, Farley D, Hogan CJ, Auld DS, Silver SJ. Generation of High-Throughput Three-Dimensional Tumor Spheroids for Drug Screening. J Vis Exp 2018. [PMID: 30247463 DOI: 10.3791/57476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cancer cells have routinely been cultured in two dimensions (2D) on a plastic surface. This technique, however, lacks the true environment a tumor mass is exposed to in vivo. Solid tumors grow not as a sheet attached to plastic, but instead as a collection of clonal cells in a three-dimensional (3D) space interacting with their neighbors, and with distinct spatial properties such as the disruption of normal cellular polarity. These interactions cause 3D-cultured cells to acquire morphological and cellular characteristics which are more relevant to in vivo tumors. Additionally, a tumor mass is in direct contact with other cell types such as stromal and immune cells, as well as the extracellular matrix from all other cell types. The matrix deposited is comprised of macromolecules such as collagen and fibronectin. In an attempt to increase the translation of research findings in oncology from bench to bedside, many groups have started to investigate the use of 3D model systems in their drug development strategies. These systems are thought to be more physiologically relevant because they attempt to recapitulate the complex and heterogeneous environment of a tumor. These systems, however, can be quite complex, and, although amenable to growth in 96-well formats, and some now even in 384, they offer few choices for large-scale growth and screening. This observed gap has led to the development of the methods described here in detail to culture tumor spheroids in a high-throughput capacity in 1536-well plates. These methods represent a compromise to the highly complex matrix-based systems, which are difficult to screen, and conventional 2D assays. A variety of cancer cell lines harboring different genetic mutations are successfully screened, examining compound efficacy by using a curated library of compounds targeting the Mitogen-Activated Protein Kinase or MAPK pathway. The spheroid culture responses are then compared to the response of cells grown in 2D, and differential activities are reported. These methods provide a unique protocol for testing compound activity in a high-throughput 3D setting.
Collapse
Affiliation(s)
- Lesley Mathews Griner
- Oncology Drug Discovery: Molecular Pharmacology, Novartis Institutes for Biomedical Research;
| | - Kalyani Gampa
- Oncology Drug Discovery: Molecular Pharmacology, Novartis Institutes for Biomedical Research
| | - Toan Do
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - Huyen Nguyen
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - David Farley
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - Christopher J Hogan
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - Douglas S Auld
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - Serena J Silver
- Oncology Drug Discovery: Molecular Pharmacology, Novartis Institutes for Biomedical Research
| |
Collapse
|
12
|
Abstract
Flow cytometry (FC) provides high-content data for a variety of applications, including phenotypic analysis of cell surface and intracellular markers, characterization of cell supernatant or lysates, and gene expression analysis. Historically, sample preparation, acquisition, and analysis have presented as a bottleneck for running such types of assays at scale. This article will outline the solutions that have been implemented at Novartis which have allowed high-throughput FC to be successfully conducted and analyzed for a variety of cell-based assays. While these experiments were generally conducted to measure phenotypic responses from a well-characterized and information-rich small molecular probe library known as the Mechanism-of-Action (MoA) Box, they are broadly applicable to any type of test sample. The article focuses on application of automated methods for FC sample preparation in 384-well assay plates. It also highlights a pipeline for analyzing large volumes of FC data, covering a visualization approach that facilitates review of screen-level data by dynamically embedding FlowJo (FJ) workspace images for each sample into a Spotfire file, directly linking them to the metric being observed. Finally, an application of these methods to a screen for MHC-I expression upregulators is discussed.
Collapse
Affiliation(s)
- Aaron C Wilson
- 1 Novartis Institutes of Biomedical Research, Cambridge, MA, USA
| | | | - Gary Yu
- 1 Novartis Institutes of Biomedical Research, Cambridge, MA, USA
| | - Javier J Pineda
- 2 Department Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Yan Feng
- 1 Novartis Institutes of Biomedical Research, Cambridge, MA, USA
| | - Douglas S Auld
- 1 Novartis Institutes of Biomedical Research, Cambridge, MA, USA
| |
Collapse
|
13
|
Auld DS, Narahari J, Ho PI, Casalena D, Nguyen V, Cirbaite E, Hughes D, Daly J, Webb B. Characterization and Use of TurboLuc Luciferase as a Reporter for High-Throughput Assays. Biochemistry 2018; 57:4700-4706. [PMID: 29641191 DOI: 10.1021/acs.biochem.8b00290] [Citation(s) in RCA: 13] [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] [Indexed: 01/30/2023]
Abstract
Luciferase-based reporter assays are powerful tools for monitoring gene expression in cells because of their ultrasensitive detection capacity and wide dynamic range. Here we describe the characterization and use of a luciferase reporter enzyme derived from the marine copepod Metridia luciferase family, referred to as TurboLuc luciferase (TurboLuc). To develop TurboLuc, the wild-type luciferase was modified to decrease its size, increase brightness, slow luminescent signal decay, and provide for efficient intracellular expression. To determine the enzyme susceptibility to compound inhibition and judge the suitability of using of TurboLuc as a reporter in screening assays, purified TurboLuc enzyme was screened for inhibitors using two different compound libraries. No inhibitors of this enzyme were identified in a library representative of typical diverse low molecular weight (LMW) compounds using a purified TurboLuc enzyme assay supporting that such libraries will show very low interference with this enzyme. We were able to identify a few inhibitors from a purified natural product library which can serve as useful tools to validate assays using TurboLuc. In addition to the inhibitor profile for TurboLuc we describe the use of this reporter in cells employing miniaturized assay volumes within 1536-well plates. TurboLuc luciferase is the smallest luciferase reporter enzyme described to date (16 kDa), shows bright luminescence and low interference by LMW compounds, and therefore should provide an ideal reporter in assays applied to high-throughput screening.
Collapse
Affiliation(s)
- Douglas S Auld
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts , United States
| | - Janaki Narahari
- Thermo Fisher Scientific , Rockford , Illinois , United States
| | - Pei-I Ho
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts , United States
| | - Dominick Casalena
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts , United States
| | - Vy Nguyen
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts , United States
| | | | - Doug Hughes
- Thermo Fisher Scientific , Rockford , Illinois , United States
| | - John Daly
- Gene Stream Pty Ltd , Perth , Australia
| | - Brian Webb
- Thermo Fisher Scientific , Rockford , Illinois , United States
| |
Collapse
|
14
|
Davis MI, Pragani R, Fox JT, Shen M, Parmar K, Gaudiano EF, Liu L, Tanega C, McGee L, Hall MD, McKnight C, Shinn P, Nelson H, Chattopadhyay D, D'Andrea AD, Auld DS, DeLucas LJ, Li Z, Boxer MB, Simeonov A. Small Molecule Inhibition of the Ubiquitin-specific Protease USP2 Accelerates cyclin D1 Degradation and Leads to Cell Cycle Arrest in Colorectal Cancer and Mantle Cell Lymphoma Models. J Biol Chem 2016; 291:24628-24640. [PMID: 27681596 DOI: 10.1074/jbc.m116.738567] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [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: 05/16/2016] [Revised: 09/04/2016] [Indexed: 12/11/2022] Open
Abstract
Deubiquitinases are important components of the protein degradation regulatory network. We report the discovery of ML364, a small molecule inhibitor of the deubiquitinase USP2 and its use to interrogate the biology of USP2 and its putative substrate cyclin D1. ML364 has an IC50 of 1.1 μm in a biochemical assay using an internally quenched fluorescent di-ubiquitin substrate. Direct binding of ML364 to USP2 was demonstrated using microscale thermophoresis. ML364 induced an increase in cellular cyclin D1 degradation and caused cell cycle arrest as shown in Western blottings and flow cytometry assays utilizing both Mino and HCT116 cancer cell lines. ML364, and not the inactive analog 2, was antiproliferative in cancer cell lines. Consistent with the role of cyclin D1 in DNA damage response, ML364 also caused a decrease in homologous recombination-mediated DNA repair. These effects by a small molecule inhibitor support a key role for USP2 as a regulator of cell cycle, DNA repair, and tumor cell growth.
Collapse
Affiliation(s)
- Mindy I Davis
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Rajan Pragani
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Jennifer T Fox
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Min Shen
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Kalindi Parmar
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Emily F Gaudiano
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Li Liu
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Cordelle Tanega
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Lauren McGee
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Matthew D Hall
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Crystal McKnight
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Paul Shinn
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Henrike Nelson
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Debasish Chattopadhyay
- the Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Alan D D'Andrea
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Douglas S Auld
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Larry J DeLucas
- the Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Zhuyin Li
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Matthew B Boxer
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892,.
| | - Anton Simeonov
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892,.
| |
Collapse
|
15
|
Auld DS, Jimenez M, Yue K, Busby S, Chen YC, Bowes S, Wendel G, Smith T, Zhang JH. Matrix-Based Activity Pattern Classification as a Novel Method for the Characterization of Enzyme Inhibitors Derived from High-Throughput Screening. ACTA ACUST UNITED AC 2016; 21:1075-1089. [DOI: 10.1177/1087057116667255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
One of the central questions in the characterization of enzyme inhibitors is determining the mode of inhibition (MOI). Classically, this is done with a number of low-throughput methods in which inhibition models are fitted to the data. The ability to rapidly characterize the MOI for inhibitors arising from high-throughput screening in which hundreds to thousands of primary inhibitors may need to be characterized would greatly help in lead selection efforts. Here we describe a novel method for determining the MOI of a compound without the need for curve fitting of the enzyme inhibition data. We provide experimental data to demonstrate the utility of this new high-throughput MOI classification method based on nonparametric analysis of the activity derived from a small matrix of substrate and inhibitor concentrations (e.g., from a 4S × 4I matrix). Lists of inhibitors from four different enzyme assays are studied, and the results are compared with the previously described IC50-shift method for MOI classification. The MOI results from this method are in good agreement with the known MOI and compare favorably with those from the IC50-shift method. In addition, we discuss some advantages and limitations of the method and provide recommendations for utilization of this MOI classification method.
Collapse
Affiliation(s)
- Douglas S. Auld
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
| | - Marta Jimenez
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
| | - Kimberley Yue
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
| | - Scott Busby
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
| | - Yu-Chi Chen
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Scott Bowes
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
| | - Greg Wendel
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
| | - Thomas Smith
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
| | - Ji-Hu Zhang
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, MA, USA
| |
Collapse
|
16
|
Davis MI, Auld DS, Inglese J. Bioluminescence Methods for Assaying Kinases in Quantitative High-Throughput Screening (qHTS) Format Applied to Yes1 Tyrosine Kinase, Glucokinase, and PI5P4Kα Lipid Kinase. Methods Mol Biol 2016; 1360:47-58. [PMID: 26501901 DOI: 10.1007/978-1-4939-3073-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Assays in which the detection of a biological phenomenon is coupled to the production of bioluminescence by luciferase have gained widespread use. As firefly luciferases (FLuc) and kinases share a common substrate (ATP), coupling of a kinase to FLuc allows for the amount of ATP remaining following a kinase reaction to be assessed by quantitating the amount of luminescence produced. Alternatively, the amount of ADP produced by the kinase reaction can be coupled to FLuc through a two-step process. This chapter describes the bioluminescent assays that were developed for three classes of kinases (lipid, protein, and metabolic kinases) and miniaturized to 1536-well format, enabling their use for quantitative high-throughput (qHTS) of small-molecule libraries.
Collapse
Affiliation(s)
- Mindy I Davis
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Douglas S Auld
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
| |
Collapse
|
17
|
Auld DS, Davis CA, Jimenez M, Knight S, Orme JP. Examining Ligand-Based Stabilization of Proteins in Cells with MEK1 Kinase Inhibitors. Assay Drug Dev Technol 2015; 13:266-76. [DOI: 10.1089/adt.2014.614] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Douglas S. Auld
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, Massachusetts
| | - Christopher A. Davis
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, Massachusetts
| | - Marta Jimenez
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, Massachusetts
| | - Sinead Knight
- AstraZeneca, R&D, Innovative Medicines, Macclesfield, Cheshire, United Kingdom
| | - Jonathon P. Orme
- AstraZeneca, R&D, Innovative Medicines, Macclesfield, Cheshire, United Kingdom
| |
Collapse
|
18
|
Liu L, Tang M, Walsh MJ, Brimacombe KR, Pragani R, Tanega C, Rohde JM, Baker HL, Fernandez E, Blackman B, Bougie JM, Leister WH, Auld DS, Shen M, Lai K, Boxer MB. Structure activity relationships of human galactokinase inhibitors. Bioorg Med Chem Lett 2014; 25:721-7. [PMID: 25553891 DOI: 10.1016/j.bmcl.2014.11.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 11/30/2022]
Abstract
Classic Galactosemia is a rare inborn error of metabolism that is caused by deficiency of galactose-1-phosphate uridyltransferase (GALT), an enzyme within the Leloir pathway that is responsible for the conversion of galactose-1-phosphate (gal-1-p) and UDP-glucose to glucose-1-phosphate and UDP-galactose. This deficiency results in elevated intracellular concentrations of its substrate, gal-1-p, and this increased concentration is believed to be the major pathogenic mechanism in Classic Galactosemia. Galactokinase (GALK) is an upstream enzyme of GALT in the Leloir pathway and is responsible for conversion of galactose and ATP to gal-1-p and ADP. Therefore, it was hypothesized that the identification of a small-molecule inhibitor of human GALK would act to prevent the accumulation of gal-1-p and offer a novel entry therapy for this disorder. Herein we describe a quantitative high-throughput screening campaign that identified a single chemotype that was optimized and validated as a GALK inhibitor.
Collapse
Affiliation(s)
- Li Liu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Manshu Tang
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Rm 2C412 SOM, 50 N. Medical Drive, Salt Lake City, UT 84132, USA
| | - Martin J Walsh
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Kyle R Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Rajan Pragani
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Cordelle Tanega
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Jason M Rohde
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Heather L Baker
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Elizabeth Fernandez
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Burchelle Blackman
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - James M Bougie
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - William H Leister
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Douglas S Auld
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Kent Lai
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Rm 2C412 SOM, 50 N. Medical Drive, Salt Lake City, UT 84132, USA
| | - Matthew B Boxer
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA.
| |
Collapse
|
19
|
Bill A, Popa MO, van Diepen MT, Gutierrez A, Lilley S, Velkova M, Acheson K, Choudhury H, Renaud NA, Auld DS, Gosling M, Groot-Kormelink PJ, Gaither LA. Variomics screen identifies the re-entrant loop of the calcium-activated chloride channel ANO1 that facilitates channel activation. J Biol Chem 2014; 290:889-903. [PMID: 25425649 DOI: 10.1074/jbc.m114.618140] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 11/06/2022] Open
Abstract
The calcium-activated chloride channel ANO1 regulates multiple physiological processes. However, little is known about the mechanism of channel gating and regulation of ANO1 activity. Using a high-throughput, random mutagenesis-based variomics screen, we generated and functionally characterized ∼6000 ANO1 mutants and identified novel mutations that affected channel activity, intracellular trafficking, or localization of ANO1. Mutations such as S741T increased ANO1 calcium sensitivity and rendered ANO1 calcium gating voltage-independent, demonstrating a critical role of the re-entrant loop in coupling calcium and voltage sensitivity of ANO1 and hence in regulating ANO1 activation. Our data present the first unbiased and comprehensive study of the structure-function relationship of ANO1. The novel ANO1 mutants reported have diverse functional characteristics, providing new tools to study ANO1 function in biological systems, paving the path for a better understanding of the function of ANO1 and its role in health and diseases.
Collapse
Affiliation(s)
- Anke Bill
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - M Oana Popa
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Michiel T van Diepen
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Abraham Gutierrez
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - Sarah Lilley
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Maria Velkova
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Kathryn Acheson
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Hedaythul Choudhury
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Nicole A Renaud
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - Douglas S Auld
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - Martin Gosling
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | | | - L Alex Gaither
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139,
| |
Collapse
|
20
|
Abstract
The wealth of bioactivity information now available on low-molecular weight compounds has enabled a paradigm shift in chemical biology and early phase drug discovery efforts. Traditionally chemical libraries have been most commonly employed in screening approaches where a bioassay is used to characterize a chemical library in a random search for active samples. However, robust curating of bioassay data, establishment of ontologies enabling mining of large chemical biology datasets, and a wealth of public chemical biology information has made possible the establishment of highly annotated compound collections. Such annotated chemical libraries can now be used to build a pathway/target hypothesis and have led to a new view where chemical libraries are used to characterize a bioassay. In this article we discuss the types of compounds in these annotated libraries composed of tools, probes, and drugs. As well, we provide rationale and a few examples for how such libraries can enable phenotypic/forward chemical genomic approaches. As with any approach, there are several pitfalls that need to be considered and we also outline some strategies to avoid these.
Collapse
Affiliation(s)
- Anne Mai Wassermann
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research Cambridge, MA, USA
| | - Luiz M Camargo
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research Cambridge, MA, USA
| | - Douglas S Auld
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research Cambridge, MA, USA
| |
Collapse
|
21
|
Blackford JA, Brimacombe KR, Dougherty EJ, Pradhan M, Shen M, Li Z, Auld DS, Chow CC, Austin CP, Simons SS. Research resource: modulators of glucocorticoid receptor activity identified by a new high-throughput screening assay. Mol Endocrinol 2014; 28:1194-206. [PMID: 24850414 DOI: 10.1210/me.2014-1069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glucocorticoid steroids affect almost every type of tissue and thus are widely used to treat a variety of human pathological conditions. However, the severity of numerous side effects limits the frequency and duration of glucocorticoid treatments. Of the numerous approaches to control off-target responses to glucocorticoids, small molecules and pharmaceuticals offer several advantages. Here we describe a new, extended high-throughput screen in intact cells to identify small molecule modulators of dexamethasone-induced glucocorticoid receptor (GR) transcriptional activity. The novelty of this assay is that it monitors changes in both GR maximal activity (A(max)) and EC(50) (the position of the dexamethasone dose-response curve). Upon screening 1280 chemicals, 10 with the greatest changes in the absolute value of A(max) or EC(50) were selected for further examination. Qualitatively identical behaviors for 60% to 90% of the chemicals were observed in a completely different system, suggesting that other systems will be similarly affected by these chemicals. Additional analysis of the 10 chemicals in a recently described competition assay determined their kinetically defined mechanism and site of action. Some chemicals had similar mechanisms of action despite divergent effects on the level of the GR-induced product. These combined assays offer a straightforward method of identifying numerous new pharmaceuticals that can alter GR transactivation in ways that could be clinically useful.
Collapse
Affiliation(s)
- John A Blackford
- Steroid Hormones Section (J.A.B., E.J.D., M.P., S.S.S.), Laboratory of Endocrinology and Receptor Biology, and Laboratory of Biological Modeling (C.C.C.), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892; and National Center for Advancing Translational Sciences (K.R.B., M.S., Z.L., D.S.A., C.P.A.), National Institutes of Health, Rockville, Maryland 20892
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Davis MI, Gross S, Shen M, Straley KS, Pragani R, Lea WA, Popovici-Muller J, DeLaBarre B, Artin E, Thorne N, Auld DS, Li Z, Dang L, Boxer MB, Simeonov A. Biochemical, cellular, and biophysical characterization of a potent inhibitor of mutant isocitrate dehydrogenase IDH1. J Biol Chem 2014; 289:13717-25. [PMID: 24668804 DOI: 10.1074/jbc.m113.511030] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [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: 11/06/2022] Open
Abstract
Two mutant forms (R132H and R132C) of isocitrate dehydrogenase 1 (IDH1) have been associated with a number of cancers including glioblastoma and acute myeloid leukemia. These mutations confer a neomorphic activity of 2-hydroxyglutarate (2-HG) production, and 2-HG has previously been implicated as an oncometabolite. Inhibitors of mutant IDH1 can potentially be used to treat these diseases. In this study, we investigated the mechanism of action of a newly discovered inhibitor, ML309, using biochemical, cellular, and biophysical approaches. Substrate binding and product inhibition studies helped to further elucidate the IDH1 R132H catalytic cycle. This rapidly equilibrating inhibitor is active in both biochemical and cellular assays. The (+) isomer is active (IC50 = 68 nm), whereas the (-) isomer is over 400-fold less active (IC50 = 29 μm) for IDH1 R132H inhibition. IDH1 R132C was similarly inhibited by (+)-ML309. WT IDH1 was largely unaffected by (+)-ML309 (IC50 >36 μm). Kinetic analyses combined with microscale thermophoresis and surface plasmon resonance indicate that this reversible inhibitor binds to IDH1 R132H competitively with respect to α-ketoglutarate and uncompetitively with respect to NADPH. A reaction scheme for IDH1 R132H inhibition by ML309 is proposed in which ML309 binds to IDH1 R132H after formation of the IDH1 R132H NADPH complex. ML309 was also able to inhibit 2-HG production in a glioblastoma cell line (IC50 = 250 nm) and had minimal cytotoxicity. In the presence of racemic ML309, 2-HG levels drop rapidly. This drop was sustained until 48 h, at which point the compound was washed out and 2-HG levels recovered.
Collapse
Affiliation(s)
- Mindy I Davis
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Stefan Gross
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, and
| | - Min Shen
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | | | - Rajan Pragani
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Wendy A Lea
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | | | - Byron DeLaBarre
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, and
| | - Erin Artin
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, and
| | - Natasha Thorne
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Douglas S Auld
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892, the Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - Zhuyin Li
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Lenny Dang
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, and
| | - Matthew B Boxer
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Anton Simeonov
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892,
| |
Collapse
|
23
|
Brimacombe KR, Walsh MJ, Liu L, Vásquez-Valdivieso MG, Morgan HP, McNae I, Fothergill-Gilmore LA, Michels PAM, Auld DS, Simeonov A, Walkinshaw MD, Shen M, Boxer MB. Identification of ML251, a Potent Inhibitor of T. brucei and T. cruzi Phosphofructokinase. ACS Med Chem Lett 2014; 5:12-7. [PMID: 24900769 DOI: 10.1021/ml400259d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 07/08/2013] [Accepted: 10/30/2013] [Indexed: 11/30/2022] Open
Abstract
Human African Trypanosomiasis (HAT) is a severe, often fatal disease caused by the parasitic protist Trypanosoma brucei. The glycolytic pathway has been identified as the sole mechanism for ATP generation in the infective stage of these organisms, and several glycolytic enzymes, phosphofructokinase (PFK) in particular, have shown promise as potential drug targets. Herein, we describe the discovery of ML251, a novel nanomolar inhibitor of T. brucei PFK, and the structure-activity relationships within the series.
Collapse
Affiliation(s)
- Kyle R. Brimacombe
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Martin J. Walsh
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Li Liu
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Montserrat G. Vásquez-Valdivieso
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Hugh P. Morgan
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Iain McNae
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Linda A. Fothergill-Gilmore
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Paul A. M. Michels
- Research
Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Douglas S. Auld
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Malcolm D. Walkinshaw
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Min Shen
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew B. Boxer
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| |
Collapse
|
24
|
Zhang JH, Kang ZB, Ardayfio O, Ho PI, Smith T, Wallace I, Bowes S, Hill WA, Auld DS. Application of Titration-Based Screening for the Rapid Pilot Testing of High-Throughput Assays. ACTA ACUST UNITED AC 2013; 19:651-60. [DOI: 10.1177/1087057113512151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 10/18/2013] [Indexed: 01/20/2023]
Abstract
Pilot testing of an assay intended for high-throughput screening (HTS) with small compound sets is a necessary but often time-consuming step in the validation of an assay protocol. When the initial testing concentration is less than optimal, this can involve iterative testing at different concentrations to further evaluate the pilot outcome, which can be even more time-consuming. Quantitative HTS (qHTS) enables flexible and rapid collection of assay performance statistics, hits at different concentrations, and concentration-response curves in a single experiment. Here we describe the qHTS process for pilot testing in which eight-point concentration-response curves are produced using an interplate asymmetric dilution protocol in which the first four concentrations are used to represent the range of typical HTS screening concentrations and the last four concentrations are added for robust curve fitting to determine potency/efficacy values. We also describe how these data can be analyzed to predict the frequency of false-positives, false-negatives, hit rates, and confirmation rates for the HTS process as a function of screening concentration. By taking into account the compound pharmacology, this pilot-testing paradigm enables rapid assessment of the assay performance and choosing the optimal concentration for the large-scale HTS in one experiment.
Collapse
Affiliation(s)
- Ji-Hu Zhang
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Zhao B. Kang
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ophelia Ardayfio
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Pei-i Ho
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Thomas Smith
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Iain Wallace
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Scott Bowes
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - W. Adam Hill
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Douglas S. Auld
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| |
Collapse
|
25
|
Thomas AG, Rojas C, Tanega C, Shen M, Simeonov A, Boxer MB, Auld DS, Ferraris DV, Tsukamoto T, Slusher BS. Kinetic characterization of ebselen, chelerythrine and apomorphine as glutaminase inhibitors. Biochem Biophys Res Commun 2013; 438:243-8. [PMID: 23850693 DOI: 10.1016/j.bbrc.2013.06.110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 06/28/2013] [Indexed: 12/14/2022]
Abstract
Glutaminase catalyzes the hydrolysis of glutamine to glutamate and plays a central role in the proliferation of neoplastic cells via glutaminolysis, as well as in the generation of excitotoxic glutamate in central nervous system disorders such as HIV-associated dementia (HAD) and multiple sclerosis. Both glutaminase siRNA and glutaminase inhibition have been shown to be effective in in vitro models of cancer and HAD, suggesting a potential role for small molecule glutaminase inhibitors. However, there are no potent, selective inhibitors of glutaminase currently available. The two prototypical glutaminase inhibitors, BPTES and DON, are either insoluble or non-specific. In a search for more drug-like glutaminase inhibitors, we conducted a screen of 1280 in vivo active drugs (Library of Pharmacologically Active Compounds (LOPAC(1280))) and identified ebselen, chelerythrine and (R)-apomorphine. The newly identified inhibitors exhibited 10 to 1500-fold greater affinities than DON and BPTES and over 100-fold increased efficiency of inhibition. Although non-selective, it is noteworthy that the affinity of ebselen for glutaminase is more potent than any other activity yet described. It is possible that the previously reported biological activity seen with these compounds is due, in part, to glutaminase inhibition. Ebselen, chelerythrine and apomorphine complement the armamentarium of compounds to explore the role of glutaminase in disease.
Collapse
Key Words
- 1,2-dimethoxy-N-methyl[1,3]benzodioxolo[5,6-c]phenanthridinium
- 13-methyl-[1,3]-benzodioxolo[5,6-c]-1,3-dioxolo[4,5-i]phenanthridinium
- 2,3-dimethoxy-N-methyl[1,3]benzodioxolo[5,6-c]phenanthridinium
- 2-phenyl-1,2-benzisoselenazol-3[2H]-one
- 5,6,6a,7-tetrahydro-6-methyl-4H-dibenzo[de,g]quinoline-10,11-diol
- 5,6-dihydro-9,10-dimethoxy-benzo[g]-[1,3]benzodioxolo[5,6-a]quinolizinium
- 6-diazo-5-oxo-l-norleucine
- Apomorphine
- BPTES
- Berberine
- CNS
- Cancer
- Chelerythrine
- DON
- Ebselen
- GAC
- GLS
- Glutamate
- Glutaminase
- Glutamine
- HIV
- HIV-associated dementia (HAD)
- HRP
- KGA
- Kinetics
- LGA
- Nitidine
- Norsanguinarine
- Sanguinarine
- [1,3]-benzodioxolo[5,6-c]-1,3-dioxolo[4,5-i]phenanthridine
- bis-2-(5-phenylacetimido-1,2,4-thiadiazol-2-yl)ethyl sulfide
- c-type glutaminase
- central nervous system
- glutaminase
- horse radish peroxidase
- human immunodeficiency virus
- kidney-type glutaminase
- liver-type glutaminase
Collapse
Affiliation(s)
- Ajit G Thomas
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Coombs TC, Tanega C, Shen M, Wang JL, Auld DS, Gerritz SW, Schoenen FJ, Thomas CJ, Aubé J. Small-molecule pyrimidine inhibitors of the cdc2-like (Clk) and dual specificity tyrosine phosphorylation-regulated (Dyrk) kinases: development of chemical probe ML315. Bioorg Med Chem Lett 2013; 23:3654-61. [PMID: 23642479 PMCID: PMC3664191 DOI: 10.1016/j.bmcl.2013.02.096] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/21/2013] [Indexed: 01/17/2023]
Abstract
Substituted pyrimidine inhibitors of the Clk and Dyrk kinases have been developed, exploring structure-activity relationships around four different chemotypes. The most potent compounds have low-nanomolar inhibitory activity against Clk1, Clk2, Clk4, Dyrk1A and Dyrk1B. Kinome scans with 442 kinases using agents representing three of the chemotypes show these inhibitors to be highly selective for the Clk and Dyrk families. Further off-target pharmacological evaluation with ML315, the most selective agent, supports this conclusion.
Collapse
Affiliation(s)
- Thomas C Coombs
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, KS 66047, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Ho PI, Yue K, Pandey P, Breault L, Harbinski F, McBride AJ, Webb B, Narahari J, Karassina N, Wood KV, Hill A, Auld DS. Reporter enzyme inhibitor study to aid assembly of orthogonal reporter gene assays. ACS Chem Biol 2013; 8:1009-17. [PMID: 23485150 DOI: 10.1021/cb3007264] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Reporter gene assays (RGAs) are commonly used to measure biological pathway modulation by small molecules. Understanding how such compounds interact with the reporter enzyme is critical to accurately interpret RGA results. To improve our understanding of reporter enzymes and to develop optimal RGA systems, we investigated eight reporter enzymes differing in brightness, emission spectrum, stability, and substrate requirements. These included common reporter enzymes such as firefly luciferase (Photinus pyralis), Renilla reniformis luciferase, and β-lactamase, as well as mutated forms of R. reniformis luciferase emitting either blue- or green-shifted luminescence, a red-light emitting form of Luciola cruciata firefly luciferase, a mutated form of Gaussia princeps luciferase, and a proprietary luciferase termed "NanoLuc" derived from the luminescent sea shrimp Oplophorus gracilirostris. To determine hit rates and structure-activity relationships, we screened a collection of 42,460 PubChem compounds at 10 μM using purified enzyme preparations. We then compared hit rates and chemotypes of actives for each enzyme. The hit rates ranged from <0.1% for β-lactamase to as high as 10% for mutated forms of Renilla luciferase. Related luciferases such as Renilla luciferase mutants showed high degrees of inhibitor overlap (40-70%), while unrelated luciferases such as firefly luciferases, Gaussia luciferase, and NanoLuc showed <10% overlap. Examination of representative inhibitors in cell-based assays revealed that inhibitor-based enzyme stabilization can lead to increases in bioluminescent signal for firefly luciferase, Renilla luciferase, and NanoLuc, with shorter half-life reporters showing increased activation responses. From this study we suggest strategies to improve the construction and interpretation of assays employing these reporter enzymes.
Collapse
Affiliation(s)
| | | | | | | | | | - Aaron J. McBride
- Thermo Fisher Scientific, Rockford, Illinois, 61105-0117, United
States
| | - Brian Webb
- Thermo Fisher Scientific, Rockford, Illinois, 61105-0117, United
States
| | - Janaki Narahari
- Thermo Fisher Scientific, Rockford, Illinois, 61105-0117, United
States
| | | | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin, 53711, United States
| | | | | |
Collapse
|
28
|
Davis MI, Sasaki AT, Shen M, Emerling BM, Thorne N, Michael S, Pragani R, Boxer M, Sumita K, Takeuchi K, Auld DS, Li Z, Cantley LC, Simeonov A. A homogeneous, high-throughput assay for phosphatidylinositol 5-phosphate 4-kinase with a novel, rapid substrate preparation. PLoS One 2013; 8:e54127. [PMID: 23326584 PMCID: PMC3542272 DOI: 10.1371/journal.pone.0054127] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/05/2012] [Indexed: 12/20/2022] Open
Abstract
Phosphoinositide kinases regulate diverse cellular functions and are important targets for therapeutic development for diseases, such as diabetes and cancer. Preparation of the lipid substrate is crucial for the development of a robust and miniaturizable lipid kinase assay. Enzymatic assays for phosphoinositide kinases often use lipid substrates prepared from lyophilized lipid preparations by sonication, which result in variability in the liposome size from preparation to preparation. Herein, we report a homogeneous 1536-well luciferase-coupled bioluminescence assay for PI5P4Kα. The substrate preparation is novel and allows the rapid production of a DMSO-containing substrate solution without the need for lengthy liposome preparation protocols, thus enabling the scale-up of this traditionally difficult type of assay. The Z’-factor value was greater than 0.7 for the PI5P4Kα assay, indicating its suitability for high-throughput screening applications. Tyrphostin AG-82 had been identified as an inhibitor of PI5P4Kα by assessing the degree of phospho transfer of γ-32P-ATP to PI5P; its inhibitory activity against PI5P4Kα was confirmed in the present miniaturized assay. From a pilot screen of a library of bioactive compounds, another tyrphostin, I-OMe tyrphostin AG-538 (I-OMe-AG-538), was identified as an ATP-competitive inhibitor of PI5P4Kα with an IC50 of 1 µM, affirming the suitability of the assay for inhibitor discovery campaigns. This homogeneous assay may apply to other lipid kinases and should help in the identification of leads for this class of enzymes by enabling high-throughput screening efforts.
Collapse
Affiliation(s)
- Mindy I. Davis
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Atsuo T. Sasaki
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Hematology and Oncology, Department of Internal Medicine, Neuroscience Institute: Brain Tumor Center, University of Cincinnati, College of Medicine, Cincinnati, Ohio, United States of America
| | - Min Shen
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Brooke M. Emerling
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Natasha Thorne
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Sam Michael
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Rajan Pragani
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Matthew Boxer
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kazutaka Sumita
- Division of Hematology and Oncology, Department of Internal Medicine, Neuroscience Institute: Brain Tumor Center, University of Cincinnati, College of Medicine, Cincinnati, Ohio, United States of America
| | - Koh Takeuchi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo, Japan
| | - Douglas S. Auld
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Zhuyin Li
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Lewis C. Cantley
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Anton Simeonov
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail:
| |
Collapse
|
29
|
Abstract
The cytochrome P450 (CYP) family contains 57 enzymes in humans. The activity of CYPs against xenobiotics is a primary consideration in drug optimization efforts. Here we describe a series of bioluminescent assays that enable the rapid profiling of CYP activity against compound collections. The assays employ a coupled-enzyme format where firefly luciferase is used to measure CYP enzyme activity through metabolism of pro-luciferase substrates.
Collapse
Affiliation(s)
- Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | |
Collapse
|
30
|
Thorne N, Shen M, Lea WA, Simeonov A, Lovell S, Auld DS, Inglese J. Firefly luciferase in chemical biology: a compendium of inhibitors, mechanistic evaluation of chemotypes, and suggested use as a reporter. ACTA ACUST UNITED AC 2012; 19:1060-72. [PMID: 22921073 DOI: 10.1016/j.chembiol.2012.07.015] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 06/25/2012] [Accepted: 07/19/2012] [Indexed: 12/20/2022]
Abstract
Firefly luciferase (FLuc) is frequently used as a reporter in high-throughput screening assays, owing to the exceptional sensitivity, dynamic range, and rapid measurement that bioluminescence affords. However, interaction of small molecules with FLuc has, to some extent, confounded its use in chemical biology and drug discovery. To identify and characterize chemotypes interacting with FLuc, we determined potency values for 360,864 compounds found in the NIH Molecular Libraries Small Molecule Repository, available in PubChem. FLuc inhibitory activity was observed for 12% of this library with discernible SAR. Characterization of 151 inhibitors demonstrated a variety of inhibition modes, including FLuc-catalyzed formation of multisubstrate adduct enzyme inhibitor complexes. As in some cell-based FLuc reporter assays, compounds acting as FLuc inhibitors yield paradoxical luminescence increases, thus data on compounds acquired from FLuc-dependent assays require careful analysis as described here.
Collapse
Affiliation(s)
- Natasha Thorne
- National Center for Advancing Translational Sciences, Bethesda, MD 20892-3370, USA
| | | | | | | | | | | | | |
Collapse
|
31
|
Anastasiou D, Yu Y, Israelsen WJ, Jiang JK, Boxer MB, Hong BS, Tempel W, Dimov S, Shen M, Jha A, Yang H, Mattaini KR, Metallo CM, Fiske BP, Courtney KD, Malstrom S, Khan TM, Kung C, Skoumbourdis AP, Veith H, Southall N, Walsh MJ, Brimacombe KR, Leister W, Lunt SY, Johnson ZR, Yen KE, Kunii K, Davidson SM, Christofk HR, Austin CP, Inglese J, Harris MH, Asara JM, Stephanopoulos G, Salituro FG, Jin S, Dang L, Auld DS, Park HW, Cantley LC, Thomas CJ, Vander Heiden MG. Erratum: Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis. Nat Chem Biol 2012. [DOI: 10.1038/nchembio1212-1008b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
32
|
Morgan HP, Walsh MJ, Blackburn EA, Wear MA, Boxer MB, Shen M, Mcnae IW, Nowicki MW, Michels PAM, Auld DS, Fothergill-Gilmore LA, Walkinshaw MD. A new family of covalent inhibitors block nucleotide binding to the active site of pyruvate kinase. Biochem J 2012; 448:67-72. [PMID: 22906073 PMCID: PMC3498827 DOI: 10.1042/bj20121014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PYK (pyruvate kinase) plays a central role in the metabolism of many organisms and cell types, but the elucidation of the details of its function in a systems biology context has been hampered by the lack of specific high-affinity small-molecule inhibitors. High-throughput screening has been used to identify a family of saccharin derivatives which inhibit LmPYK (Leishmania mexicana PYK) activity in a time- (and dose-) dependent manner, a characteristic of irreversible inhibition. The crystal structure of DBS {4-[(1,1-dioxo-1,2-benzothiazol-3-yl)sulfanyl]benzoic acid} complexed with LmPYK shows that the saccharin moiety reacts with an active-site lysine residue (Lys335), forming a covalent bond and sterically hindering the binding of ADP/ATP. Mutation of the lysine residue to an arginine residue eliminated the effect of the inhibitor molecule, providing confirmation of the proposed inhibitor mechanism. This lysine residue is conserved in the active sites of the four human PYK isoenzymes, which were also found to be irreversibly inhibited by DBS. X-ray structures of PYK isoforms show structural differences at the DBS-binding pocket, and this covalent inhibitor of PYK provides a chemical scaffold for the design of new families of potentially isoform-specific irreversible inhibitors.
Collapse
Affiliation(s)
- Hugh P. Morgan
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Martin J. Walsh
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human, Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, U.S.A
| | - Elizabeth A. Blackburn
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Martin A. Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Matthew B. Boxer
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human, Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, U.S.A
| | - Min Shen
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human, Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, U.S.A
| | - Iain W. Mcnae
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Matthew W. Nowicki
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Paul A. M. Michels
- Research Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Douglas S. Auld
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human, Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, U.S.A
| | - Linda A. Fothergill-Gilmore
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Malcolm D. Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| |
Collapse
|
33
|
Smith T, Ho PI, Yue K, Itkin Z, MacDougall D, Paolucci M, Hill A, Auld DS. Comparison of compound administration methods in biochemical assays: effects on apparent compound potency using either assay-ready compound plates or pin tool-delivered compounds. ACTA ACUST UNITED AC 2012; 18:14-25. [PMID: 22904199 DOI: 10.1177/1087057112455434] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Compound sample preparation and delivery are the most critical steps in high-throughput screening (HTS) campaigns. Historically, several methods of compound delivery to assays have been used for HTS, including intermediate plates with prediluted compounds, assay-ready plates (ARPs) using either preplated dried compound films or nanoliter DMSO spots of compounds, as well as pin tool-delivered compounds. We and others have observed differences in apparent compound potency depending on the compound delivery method. To quantitatively measure compound potency differences due to the chosen delivery methods, we conducted a controlled study using a validated biochemical luciferase assay and compared potencies when compounds were delivered in either ARPs (using acoustic dispensed nanoliter spots) or by pin tool. Here we compare hit rates, confirmation rates, false-positive rates, and false-negative rates between the two delivery methods using the luciferase assay. We compared polystyrene (PS) and cyclic olefin copolymer (COC) plates using both delivery methods and examined whether ARPs stored at 4 °C were superior to those stored frozen at -20 °C. The data show that the choice of compound delivery method to the assay has an effect on the apparent IC(50)'s and that pin tool delivery results in more confirmed hits than preplated compounds, resulting in a lower false-negative rate. However, this effect is minimized through the use of COC plates and by obtaining plates in a "just-in-time" mode. Overall, this report provides guidance on using assay-ready compound plates and has affected the way HTS campaigns are using acoustically dispensed plates in our department.
Collapse
Affiliation(s)
- Thomas Smith
- Lead Finding Platform, Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Inc., Cambridge, MA 02139, USA.
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Cruz PG, Auld DS, Schultz PJ, Lovell S, Battaile KP, MacArthur R, Shen M, Tamayo-Castillo G, Inglese J, Sherman DH. Titration-based screening for evaluation of natural product extracts: identification of an aspulvinone family of luciferase inhibitors. ACTA ACUST UNITED AC 2012; 18:1442-52. [PMID: 22118678 DOI: 10.1016/j.chembiol.2011.08.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/18/2011] [Accepted: 08/09/2011] [Indexed: 10/15/2022]
Abstract
The chemical diversity of nature has tremendous potential for the discovery of molecular probes and medicinal agents. However, sensitivity of HTS assays to interfering components of crude extracts derived from plants, and macro- and microorganisms has curtailed their use in lead discovery. Here, we describe a process for leveraging the concentration-response curves obtained from quantitative HTS to improve the initial selection of "actives" from a library of partially fractionated natural product extracts derived from marine actinomycetes and fungi. By using pharmacological activity, the first-pass CRC paradigm improves the probability that labor-intensive subsequent steps of reculturing, extraction, and bioassay-guided isolation of active component(s) target the most promising strains and growth conditions. We illustrate how this process identified a family of fungal metabolites as potent inhibitors of firefly luciferase, subsequently resolved in molecular detail by X-ray crystallography.
Collapse
Affiliation(s)
- Patricia G Cruz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Anastasiou D, Poulogiannis G, Asara JM, Boxer MB, Jiang JK, Shen M, Bellinger G, Sasaki AT, Locasale JW, Auld DS, Thomas CJ, Vander Heiden MG, Cantley LC. Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses. Science 2011; 334:1278-83. [PMID: 22052977 DOI: 10.1126/science.1211485] [Citation(s) in RCA: 856] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Control of intracellular reactive oxygen species (ROS) concentrations is critical for cancer cell survival. We show that, in human lung cancer cells, acute increases in intracellular concentrations of ROS caused inhibition of the glycolytic enzyme pyruvate kinase M2 (PKM2) through oxidation of Cys(358). This inhibition of PKM2 is required to divert glucose flux into the pentose phosphate pathway and thereby generate sufficient reducing potential for detoxification of ROS. Lung cancer cells in which endogenous PKM2 was replaced with the Cys(358) to Ser(358) oxidation-resistant mutant exhibited increased sensitivity to oxidative stress and impaired tumor formation in a xenograft model. Besides promoting metabolic changes required for proliferation, the regulatory properties of PKM2 may confer an additional advantage to cancer cells by allowing them to withstand oxidative stress.
Collapse
Affiliation(s)
- Dimitrios Anastasiou
- Beth Israel Deaconess Medical Center, Department of Medicine-Division of Signal Transduction, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
de Kruijf P, Lim HD, Roumen L, Renjaän VA, Zhao J, Webb ML, Auld DS, Wijkmans JC, Zaman GJR, Smit MJ, de Graaf C, Leurs R. Identification of a Novel Allosteric Binding Site in the CXCR2 Chemokine Receptor. Mol Pharmacol 2011; 80:1108-18. [DOI: 10.1124/mol.111.073825] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
37
|
Walsh MJ, Brimacombe KR, Veith H, Bougie JM, Daniel T, Leister W, Cantley LC, Israelsen WJ, Vander Heiden MG, Shen M, Auld DS, Thomas CJ, Boxer MB. 2-Oxo-N-aryl-1,2,3,4-tetrahydroquinoline-6-sulfonamides as activators of the tumor cell specific M2 isoform of pyruvate kinase. Bioorg Med Chem Lett 2011; 21:6322-7. [PMID: 21958545 DOI: 10.1016/j.bmcl.2011.08.114] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 12/20/2022]
Abstract
Compared to normal differentiated cells, cancer cells have altered metabolic regulation to support biosynthesis and the expression of the M2 isozyme of pyruvate kinase (PKM2) plays an important role in this anabolic metabolism. While the M1 isoform is a highly active enzyme, the alternatively spliced M2 variant is considerably less active and expressed in tumors. While the exact mechanism by which decreased pyruvate kinase activity contributes to anabolic metabolism remains unclear, it is hypothesized that activation of PKM2 to levels seen with PKM1 may promote a metabolic program that is not conducive to cell proliferation. Here we report the third chemotype in a series of PKM2 activators based on the 2-oxo-N-aryl-1,2,3,4-tetrahydroquinoline-6-sulfonamide scaffold. The synthesis, structure activity relationships, selectivity and notable physiochemical properties are described.
Collapse
Affiliation(s)
- Martin J Walsh
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Morgan HP, McNae IW, Nowicki MW, Zhong W, Michels PAM, Auld DS, Fothergill-Gilmore LA, Walkinshaw MD. The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site. J Biol Chem 2011; 286:31232-40. [PMID: 21733839 PMCID: PMC3173065 DOI: 10.1074/jbc.m110.212613] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 06/06/2011] [Indexed: 11/06/2022] Open
Abstract
Ehrlich's pioneering chemotherapeutic experiments published in 1904 (Ehrlich, P., and Shiga, K. (1904) Berlin Klin. Wochenschrift 20, 329-362) described the efficacy of a series of dye molecules including trypan blue and trypan red to eliminate trypanosome infections in mice. The molecular structures of the dyes provided a starting point for the synthesis of suramin, which was developed and used as a trypanocidal drug in 1916 and is still in clinical use. Despite the biological importance of these dye-like molecules, the mode of action on trypanosomes has remained elusive. Here we present crystal structures of suramin and three related dyes in complex with pyruvate kinases from Leishmania mexicana or from Trypanosoma cruzi. The phenyl sulfonate groups of all four molecules (suramin, Ponceau S, acid blue 80, and benzothiazole-2,5-disulfonic acid) bind in the position of ADP/ATP at the active sites of the pyruvate kinases (PYKs). The binding positions in the two different trypanosomatid PYKs are nearly identical. We show that suramin competitively inhibits PYKs from humans (muscle, tumor, and liver isoenzymes, K(i) = 1.1-17 μM), T. cruzi (K(i) = 108 μM), and L. mexicana (K(i) = 116 μM), all of which have similar active sites. Synergistic effects were observed when examining suramin inhibition in the presence of an allosteric effector molecule, whereby IC(50) values decreased up to 2-fold for both trypanosomatid and human PYKs. These kinetic and structural analyses provide insight into the promiscuous inhibition observed for suramin and into the mode of action of the dye-like molecules used in Ehrlich's original experiments.
Collapse
Affiliation(s)
- Hugh P. Morgan
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Iain W. McNae
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Matthew W. Nowicki
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Wenhe Zhong
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Paul A. M. Michels
- the Research Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium, and
| | - Douglas S. Auld
- the National Institutes of Health Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20850
| | - Linda A. Fothergill-Gilmore
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Malcolm D. Walkinshaw
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| |
Collapse
|
39
|
Rosenthal AS, Tanega C, Shen M, Mott BT, Bougie JM, Nguyen DT, Misteli T, Auld DS, Maloney DJ, Thomas CJ. Potent and selective small molecule inhibitors of specific isoforms of Cdc2-like kinases (Clk) and dual specificity tyrosine-phosphorylation-regulated kinases (Dyrk). Bioorg Med Chem Lett 2011; 21:3152-8. [PMID: 21450467 PMCID: PMC3085634 DOI: 10.1016/j.bmcl.2011.02.114] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 02/24/2011] [Accepted: 02/28/2011] [Indexed: 11/22/2022]
Abstract
Continued examination of substituted 6-arylquinazolin-4-amines as Clk4 inhibitors resulted in selective inhibitors of Clk1, Clk4, Dyrk1A and Dyrk1B. Several of the most potent inhibitors were validated as being highly selective within a comprehensive kinome scan.
Collapse
Affiliation(s)
- Andrew S. Rosenthal
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Cordelle Tanega
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Min Shen
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Bryan T. Mott
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - James M. Bougie
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Dac-Trung Nguyen
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, NIH, 41 Library Drive, Bethesda, MD 20892 USA
| | - Douglas S. Auld
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - David J. Maloney
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Craig J. Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| |
Collapse
|
40
|
Napier SE, Letourneau JJ, Ansari N, Auld DS, Baker J, Best S, Campbell-Wan L, Chan JH, Craighead M, Desai H, Goan KA, Ho KK, Hulskotte EG, MacSweeney CP, Milne R, Morphy JR, Neagu I, Ohlmeyer MH, Peeters AW, Presland J, Riviello C, Ruigt GS, Thomson FJ, Zanetakos HA, Zhao J, Webb ML. Synthesis and SAR studies of novel 2-(4-oxo-2-aryl-quinazolin-3(4H)-yl)acetamide vasopressin V1b receptor antagonists. Bioorg Med Chem Lett 2011; 21:1871-5. [DOI: 10.1016/j.bmcl.2010.12.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/14/2010] [Accepted: 12/16/2010] [Indexed: 11/26/2022]
|
41
|
Shukla SJ, Sakamuru S, Huang R, Moeller TA, Shinn P, Vanleer D, Auld DS, Austin CP, Xia M. Identification of clinically used drugs that activate pregnane X receptors. Drug Metab Dispos 2010; 39:151-9. [PMID: 20966043 DOI: 10.1124/dmd.110.035105] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The pregnane X receptor (PXR) binds xenobiotics and regulates the expression of several drug-metabolizing enzymes and transporters. Human PXR (hPXR) activation and CYP3A4 induction can be involved in drug-drug interactions, resulting in reduced efficacy or increased toxicity. However, there are known species-specific differences with regard to PXR activation that should be taken into account when animal PXR data are extrapolated to humans. We profiled 2816 clinically used drugs from the National Institutes of Health Chemical Genomics Center Pharmaceutical Collection for their ability to activate hPXR and rat PXR (rPXR) at the cellular level, induce human CYP3A4 at the cellular level, and bind human PXR at the protein level. From 6 to 11% of drugs were identified as active across the four assays, which included assay-specific and pan-active compounds. The lowest concordance was observed between the hPXR and rPXR assays, and many compounds active in both assays nonetheless demonstrated significant potency differences between species. Analysis based on clustering potency values demonstrated the greatest activity correlation between the hPXR activation and CYP3A4 induction assays. Structure-activity relationship analysis identified chemical scaffolds that were pan-active (e.g., dihydropyridine calcium channel blockers) and others that were uniquely active in individual assays (e.g., steroids and fatty acids). These results provide important information on PXR activation by clinically used drugs, highlight the species specificity of PXR activation by xenobiotics, and provide a means of prioritizing compounds for follow-up studies and optimization efforts.
Collapse
Affiliation(s)
- Sunita J Shukla
- National Institutes of Health Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Thomas CJ, Auld DS, Huang R, Huang W, Jadhav A, Johnson RL, Leister W, Maloney DJ, Marugan JJ, Michael S, Simeonov A, Southall N, Xia M, Zheng W, Inglese J, Austin CP. The pilot phase of the NIH Chemical Genomics Center. Curr Top Med Chem 2010; 9:1181-93. [PMID: 19807664 DOI: 10.2174/156802609789753644] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 11/24/2009] [Indexed: 01/28/2023]
Abstract
The NIH Chemical Genomics Center (NCGC) was the inaugural center of the Molecular Libraries and Screening Center Network (MLSCN). Along with the nine other research centers of the MLSCN, the NCGC was established with a primary goal of bringing industrial technology and experience to empower the scientific community with small molecule compounds for use in their research. We intend this review to serve as 1) an introduction to the NCGC standard operating procedures, 2) an overview of several of the lessons learned during the pilot phase and 3) a review of several of the innovative discoveries reported during the pilot phase of the MLSCN.
Collapse
Affiliation(s)
- Craig J Thomas
- NIH Chemical Genomics Center, NHGRI, National Institutes of Health, 9800 Medical Center Drive, Building B, Room 3005, MSC: 3370, Bethesda, MD 20892-3370, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Letourneau JJ, Riviello CM, Li H, Cole AG, Ho KK, Zanetakos HA, Desai H, Zhao J, Auld DS, Napier SE, Thomson FJ, Goan KA, Morphy JR, Ohlmeyer MH, Webb ML. Identification and optimization of novel 2-(4-oxo-2-aryl-quinazolin-3(4H)-yl)acetamide vasopressin V3 (V1b) receptor antagonists. Bioorg Med Chem Lett 2010; 20:5394-7. [DOI: 10.1016/j.bmcl.2010.07.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/21/2010] [Accepted: 07/26/2010] [Indexed: 11/27/2022]
|
44
|
Thorne N, Auld DS, Inglese J. Apparent activity in high-throughput screening: origins of compound-dependent assay interference. Curr Opin Chem Biol 2010; 14:315-24. [PMID: 20417149 PMCID: PMC2878863 DOI: 10.1016/j.cbpa.2010.03.020] [Citation(s) in RCA: 304] [Impact Index Per Article: 21.7] [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] [Received: 01/15/2010] [Revised: 02/27/2010] [Accepted: 03/21/2010] [Indexed: 12/25/2022]
Abstract
Expansive compound collections made up of structurally heterogeneous chemicals, the activities of which are largely undefined, present challenging problems for high-throughput screening (HTS). Foremost is differentiating whether the activity for a given compound in an assay is directed against the targeted biology, or is the result of surreptitious compound activity involving the assay detection system. Such compound interference can be especially difficult to identify if it is reproducible and concentration-dependent - characteristics generally attributed to compounds with genuine activity. While reactive chemical groups on compounds were once thought to be the primary source of compound interference in assays used in HTS, recent work suggests that other factors, such as compound aggregation, may play a more significant role in many assay formats. Considerable progress has been made to profile representative compound libraries in an effort to identify chemical classes susceptible to producing compound interference, such as compounds commonly found to inhibit the reporter enzyme firefly luciferase. Such work has also led to the development of practices that have the potential to significantly reduce compound interference, for example, through the addition of non-ionic detergent to assay buffer to reduce aggregation-based inhibition.
Collapse
Affiliation(s)
- Natasha Thorne
- NIH Chemical Genomics Center, National Institutes of Health, Bethesda, MD 20892-3370, USA
| | - Douglas S. Auld
- NIH Chemical Genomics Center, National Institutes of Health, Bethesda, MD 20892-3370, USA
| | - James Inglese
- NIH Chemical Genomics Center, National Institutes of Health, Bethesda, MD 20892-3370, USA
| |
Collapse
|
45
|
Boxer MB, Quinn AM, Shen M, Jadhav A, Leister W, Simeonov A, Auld DS, Thomas CJ. A highly potent and selective caspase 1 inhibitor that utilizes a key 3-cyanopropanoic acid moiety. ChemMedChem 2010; 5:730-8. [PMID: 20229566 PMCID: PMC3062473 DOI: 10.1002/cmdc.200900531] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Indexed: 11/11/2022]
Abstract
Herein, we examine the potential of a nitrile-containing propionic acid moiety as an electrophile for covalent attack by the active-site cysteine residue of caspase 1. The syntheses of several cyanopropanate-containing small molecules based on the optimized peptidic scaffold of prodrug VX-765 were accomplished. These compounds were found to be potent inhibitors of caspase 1 (IC(50) values < or =1 nM). Examination of these novel small molecules against a caspase panel demonstrated an impressive degree of selectivity for caspase 1 inhibition over other caspase isozymes. Assessment of hydrolytic stability and selected ADME properties highlighted these agents as potentially useful tools for studying caspase 1 down-regulation in various settings, including in vivo analyses.
Collapse
Affiliation(s)
- Matthew B. Boxer
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Amy M. Quinn
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Min Shen
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - William Leister
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Douglas S. Auld
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Craig J. Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| |
Collapse
|
46
|
Shen M, Zhang Y, Wiestner AU, Ashlock MA, Austin CP, Auld DS. Abstract 3685: A strategy to identify therapeutic candidates for chronic lymphocytic leukemia from a library of FDA approved drugs. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-3685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Chronic lymphocytic leukemia (CLL) is an adult lymphoid malignancy with a variable clinical course. There is considerable interest in the identification of new treatments, as most current approaches are not curative. While most patients respond to initial chemotherapy, relapsed disease is often resistant to the drugs commonly used in CLL and are left without limited therapeutic options. In this study, we used a luminescent cell viability assay based on ATP levels (CellTiter-Glo, Promega) to find compounds that were potent and efficacious in killing CLL cells. We employed an in-house process of quantitative high throughput screening (qHTS) to assess 8-9 concentrations of each member of a 2,816 compound library (including FDA-approved drugs and those known to be bio-active from commercial suppliers). Using qHTS we generated potency values on each compound in lymphocytes donated from each of six individuals with CLL and five unaffected individuals. We found 102 compounds efficacious against cells from all six individuals with CLL (“consensus” drugs) with seven of these showing no efficacy on lymphocytes from a majority of unaffected donors, suggesting some degree of specificity for the leukemic cells. Furthermore, to determine if we could save time and cost we screened the same library using CLL cells pooled from these individuals. We found that over 90% of the 102 drugs identified as efficacious on cells from individuals were also efficacious in the pooled experiment. Importantly, a near perfect correlation was observed in potency values between the single and pooled studies. The results of this “pooling” approach suggests it is rationale to apply pooling and qHTS when screening CLL cells against much larger collections (>300,000 unapproved compounds) where novel compounds could be identified as starting points for drug discovery and development.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3685.
Collapse
Affiliation(s)
- Min Shen
- 1NIH Chemical Genomics Center, National Human Genome Research Institute, National Institute of Health, Rockville, MD
| | - Yaqin Zhang
- 1NIH Chemical Genomics Center, National Human Genome Research Institute, National Institute of Health, Rockville, MD
| | - Adrian U. Wiestner
- 2National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Melissa A. Ashlock
- 3Therapeutics for Rare and Neglected Diseases Program, National Human Genome Research Institute, National Institutes of Health, Rockville, MD
| | - Christopher P. Austin
- 1NIH Chemical Genomics Center, National Human Genome Research Institute, National Institute of Health, Rockville, MD
| | - Douglas S. Auld
- 1NIH Chemical Genomics Center, National Human Genome Research Institute, National Institute of Health, Rockville, MD
| |
Collapse
|
47
|
Tanega C, Shen M, Mott BT, Thomas CJ, MacArthur R, Inglese J, Auld DS. Comparison of bioluminescent kinase assays using substrate depletion and product formation. Assay Drug Dev Technol 2010; 7:606-14. [PMID: 20059377 DOI: 10.1089/adt.2009.0230] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Assays for ATPases have been enabled for high-throughput screening (HTS) by employing firefly luciferase to detect the remaining ATP in the assay. However, for any enzyme assay, measurement of product formation is a more sensitive assay design. Recently, technologies that allow detection of the ADP product from ATPase reactions have been described using fluorescent methods of detection. We describe here the characterization of a bioluminescent assay that employs firefly luciferase in a coupled-enzyme assay format to enable detection of ADP levels from ATPase assays (ADP-Glo, Promega Corp.). We determined the performance of the ADP-Glo assay in 1,536-well microtiter plates using the protein kinase Clk4 and a 1,352 member kinase focused combinatorial library. The ADP-Glo assay was compared to the Clk4 assay performed using a bioluminescence ATP-depletion format (Kinase-Glo, Promega Corp). We performed this analysis using quantitative HTS (qHTS) where we determined potency values for all library members and identified approximately 300 compounds with potencies ranging from as low as 50 nM to >10 microM, yielding a robust dataset for the comparison. Both assay formats showed high performance (Z'-factors approximately 0.9) and showed a similar potency distribution for the actives. We conclude that the bioluminescence ADP detection assay system is a viable generic alternative to the widely used ATP-depletion assay for ATPases and discuss the advantages and disadvantages of both approaches.
Collapse
Affiliation(s)
- Cordelle Tanega
- NIH Chemical Genomics Center, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | | | | | | | |
Collapse
|
48
|
Boxer MB, Jiang JK, Vander Heiden MG, Shen M, Skoumbourdis AP, Southall N, Veith H, Leister W, Austin CP, Park HW, Inglese J, Cantley LC, Auld DS, Thomas CJ. Evaluation of substituted N,N'-diarylsulfonamides as activators of the tumor cell specific M2 isoform of pyruvate kinase. J Med Chem 2010; 53:1048-55. [PMID: 20017496 DOI: 10.1021/jm901577g] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The metabolism of cancer cells is altered to support rapid proliferation. Pharmacological activators of a tumor cell specific pyruvate kinase isozyme (PKM2) may be an approach for altering the classic Warburg effect characteristic of aberrant metabolism in cancer cells yielding a novel antiproliferation strategy. In this manuscript, we detail the discovery of a series of substituted N,N'-diarylsulfonamides as activators of PKM2. The synthesis of numerous analogues and the evaluation of structure-activity relationships are presented as well as assessments of mechanism and selectivity. Several agents are found that have good potencies and appropriate solubility for use as chemical probes of PKM2 including 55 (AC(50) = 43 nM, maximum response = 84%; solubility = 7.3 microg/mL), 56 (AC(50) = 99 nM, maximum response = 84%; solubility = 5.7 microg/mL), and 58 (AC(50) = 38 nM, maximum response = 82%; solubility = 51.2 microg/mL). The small molecules described here represent first-in-class activators of PKM2.
Collapse
Affiliation(s)
- Matthew B Boxer
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, MSC 3370 Bethesda, Maryland 20850, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Brimacombe KR, Hall MD, Auld DS, Inglese J, Austin CP, Gottesman MM, Fung KL. A dual-fluorescence high-throughput cell line system for probing multidrug resistance. Assay Drug Dev Technol 2009; 7:233-49. [PMID: 19548831 DOI: 10.1089/adt.2008.165] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The efflux pump P-glycoprotein (ATP-binding cassette B1, multidrug resistance [MDR] 1, P-gp) has long been known to contribute to MDR against cancer chemotherapeutics. We describe the development of a dual-fluorescent cell line system to allow multiplexing of drug-sensitive and P-gp-mediated MDR cell lines. The parental OVCAR-8 human ovarian carcinoma cell line and the isogenic MDR NCI/ADR-RES subline, which stably expresses high levels of endogenous P-gp, were transfected to express the fluorescent proteins Discosoma sp. red fluorescent protein DsRed2 and enhanced green fluorescent protein, respectively. Co-culture conditions were defined, and fluorescent barcoding of each cell line allowed for the direct, simultaneous comparison of resistance to cytotoxic compounds in sensitive and MDR cell lines. We show that this assay system retains the phenotypes of the original lines and is suitable for multiplexing using confocal microscopy, flow cytometry, or laser scanning microplate cytometry in 1,536-well plates, enabling the high-throughput screening of large chemical libraries.
Collapse
Affiliation(s)
- Kyle R Brimacombe
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | | |
Collapse
|
50
|
Mott BT, Tanega C, Shen M, Maloney DJ, Shinn P, Leister W, Marugan JJ, Inglese J, Austin CP, Misteli T, Auld DS, Thomas CJ. Evaluation of substituted 6-arylquinazolin-4-amines as potent and selective inhibitors of cdc2-like kinases (Clk). Bioorg Med Chem Lett 2009; 19:6700-5. [PMID: 19837585 DOI: 10.1016/j.bmcl.2009.09.121] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 09/29/2009] [Accepted: 09/30/2009] [Indexed: 12/30/2022]
Abstract
A series of substituted 6-arylquinazolin-4-amines were prepared and analyzed as inhibitors of Clk4. Synthesis, structure-activity relationships and the selectivity of a potent analogue against a panel of 402 kinases are presented. Inhibition of Clk4 by these agents at varied concentrations of assay substrates (ATP and receptor peptide) highly suggests that this chemotype is an ATP competitive inhibitor. Molecular docking provides further evidence that inhibition is the result of binding at the kinase hinge region. Selected compounds represent novel tools capable of potent and selective inhibition of Clk1, Clk4, and Dyrk1A.
Collapse
Affiliation(s)
- Bryan T Mott
- NIH Chemical Genomics Center, National Human Genome Research Institute, Bethesda, MD 20892-3370, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|