1
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Anantharajan J, Baburajendran N, Lin G, Loh YY, Xu W, Ahmad NHB, Liu S, Jansson AE, Kuan JWL, Ng EY, Yeo YK, Hung AW, Joy J, Hill J, Ford HL, Zhao R, Keller TH, Kang C. Structure-activity relationship studies of allosteric inhibitors of EYA2 tyrosine phosphatase. Protein Sci 2022; 31:422-431. [PMID: 34761455 PMCID: PMC8819961 DOI: 10.1002/pro.4234] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/23/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 02/03/2023]
Abstract
Human eyes absent (EYA) proteins possess Tyr phosphatase activity, which is critical for numerous cancer and metastasis promoting activities, making it an attractive target for cancer therapy. In this work, we demonstrate that the inhibitor-bound form of EYA2 does not favour binding to Mg2+ , which is indispensable for the Tyr phosphatase activity. We further describe characterization and optimization of this class of allosteric inhibitors. A series of analogues were synthesized to improve potency of the inhibitors and to elucidate structure-activity relationships. Two co-crystal structures confirm the binding modes of this class of inhibitors. Our medicinal chemical, structural, biochemical, and biophysical studies provide insight into the molecular interactions of EYA2 with these allosteric inhibitors. The compounds derived from this study are useful for exploring the function of the Tyr phosphatase activity of EYA2 in normal and cancerous cells and serve as reference compounds for screening or developing allosteric phosphatase inhibitors. Finally, the co-crystal structures reported in this study will aid in structure-based drug discovery against EYA2.
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Affiliation(s)
- Jothi Anantharajan
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Nithya Baburajendran
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Grace Lin
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Yong Yao Loh
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Weijun Xu
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Nur Huda Binte Ahmad
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Shuang Liu
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
- Chemical Biology and Therapeutics ScienceBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Anna E. Jansson
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - John Wee Liang Kuan
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Elizabeth Yihui Ng
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Yee Khoon Yeo
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Alvin W. Hung
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Joma Joy
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Jeffrey Hill
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Heide L. Ford
- Department of Obstetrics and GynecologyUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Rui Zhao
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Thomas H. Keller
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - CongBao Kang
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
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2
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Yu J, Liao PJ, Xu W, Jones JR, Everman DB, Flanagan-Steet H, Keller TH, Virshup DM. Structural model of human PORCN illuminates disease-associated variants and drug-binding sites. J Cell Sci 2021; 134:273795. [PMID: 34817055 DOI: 10.1242/jcs.259383] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/11/2021] [Indexed: 12/20/2022] Open
Abstract
Wnt signaling is essential for normal development and is a therapeutic target in cancer. The enzyme PORCN, or porcupine, is a membrane-bound O-acyltransferase (MBOAT) that is required for the post-translational modification of all Wnts, adding an essential mono-unsaturated palmitoleic acid to a serine on the tip of Wnt hairpin 2. Inherited mutations in PORCN cause focal dermal hypoplasia, and therapeutic inhibition of PORCN slows the growth of Wnt-dependent cancers. Based on homology to mammalian MBOAT proteins, we developed and validated a structural model of human PORCN. The model accommodates palmitoleoyl-CoA and Wnt hairpin 2 in two tunnels in the conserved catalytic core, shedding light on the catalytic mechanism. The model predicts how previously uncharacterized human variants of uncertain significance can alter PORCN function. Drugs including ETC-159, IWP-L6 and LGK-974 dock in the PORCN catalytic site, providing insights into PORCN pharmacologic inhibition. This structural model enhances our mechanistic understanding of PORCN substrate recognition and catalysis, as well as the inhibition of its enzymatic activity, and can facilitate the development of improved inhibitors and the understanding of disease-relevant PORCN mutants. This article has an associated First Person interview with the joint first authors of the paper.
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Affiliation(s)
- Jia Yu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
| | - Pei-Ju Liao
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
| | - Weijun Xu
- Discovery Chemistry, Experimental Drug Development Centre, 10 Biopolis Road, Chromos, 138670, Singapore
| | - Julie R Jones
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - David B Everman
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Thomas H Keller
- Discovery Chemistry, Experimental Drug Development Centre, 10 Biopolis Road, Chromos, 138670, Singapore
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
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3
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Zhang G, Dong Z, Gimple RC, Wolin A, Wu Q, Qiu Z, Wood LM, Shen JZ, Jiang L, Zhao L, Lv D, Prager BC, Kim LJY, Wang X, Zhang L, Anderson RL, Moore JK, Bao S, Keller TH, Lin G, Kang C, Hamerlik P, Zhao R, Ford HL, Rich JN. Targeting EYA2 tyrosine phosphatase activity in glioblastoma stem cells induces mitotic catastrophe. J Exp Med 2021; 218:212685. [PMID: 34617969 PMCID: PMC8504185 DOI: 10.1084/jem.20202669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 07/11/2021] [Accepted: 08/19/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma ranks among the most lethal of primary brain malignancies, with glioblastoma stem cells (GSCs) at the apex of tumor cellular hierarchies. Here, to discover novel therapeutic GSC targets, we interrogated gene expression profiles from GSCs, differentiated glioblastoma cells (DGCs), and neural stem cells (NSCs), revealing EYA2 as preferentially expressed by GSCs. Targeting EYA2 impaired GSC maintenance and induced cell cycle arrest, apoptosis, and loss of self-renewal. EYA2 displayed novel localization to centrosomes in GSCs, and EYA2 tyrosine (Tyr) phosphatase activity was essential for proper mitotic spindle assembly and survival of GSCs. Inhibition of the EYA2 Tyr phosphatase activity, via genetic or pharmacological means, mimicked EYA2 loss in GSCs in vitro and extended the survival of tumor-bearing mice. Supporting the clinical relevance of these findings, EYA2 portends poor patient prognosis in glioblastoma. Collectively, our data indicate that EYA2 phosphatase function plays selective critical roles in the growth and survival of GSCs, potentially offering a high therapeutic index for EYA2 inhibitors.
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Affiliation(s)
- Guoxin Zhang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Zhen Dong
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Ryan C Gimple
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Arthur Wolin
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Qiulian Wu
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Zhixin Qiu
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Lisa M Wood
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO
| | - Jia Z Shen
- Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Li Jiang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Linjie Zhao
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Deguan Lv
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Briana C Prager
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Leo J Y Kim
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Xiuxing Wang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ryan L Anderson
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO
| | - Shideng Bao
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Thomas H Keller
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore
| | - Grace Lin
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore
| | - Petra Hamerlik
- Danish Cancer Society Research Center, Copenhagen, Denmark.,Department of Drug Design and Pharmacology, Copenhagen University, Copenhagen, Denmark
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Heide L Ford
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jeremy N Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA.,University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA.,Department of Neurology, University of Pittsburgh, Pittsburgh, PA
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4
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Quach D, Tang G, Anantharajan J, Baburajendran N, Poulsen A, Wee JLK, Retna P, Li R, Liu B, Tee DHY, Kwek PZ, Joy JK, Yang W, Zhang C, Foo K, Keller TH, Yao SQ. Strategic Design of Catalytic Lysine‐Targeting Reversible Covalent BCR‐ABL Inhibitors**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David Quach
- NUS Graduate School for Integrative Sciences and Engineering 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02 Singapore 119077 Singapore
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Guanghui Tang
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| | - Jothi Anantharajan
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - John L. K. Wee
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Priya Retna
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Rong Li
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Boping Liu
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Doris H. Y. Tee
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Perlyn Z. Kwek
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Joma K. Joy
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Wan‐Qi Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Chong‐Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Klement Foo
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Thomas H. Keller
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Shao Q. Yao
- NUS Graduate School for Integrative Sciences and Engineering 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02 Singapore 119077 Singapore
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
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5
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Quach D, Tang G, Anantharajan J, Baburajendran N, Poulsen A, Wee JLK, Retna P, Li R, Liu B, Tee DHY, Kwek PZ, Joy JK, Yang WQ, Zhang CJ, Foo K, Keller TH, Yao SQ. Strategic Design of Catalytic Lysine-Targeting Reversible Covalent BCR-ABL Inhibitors*. Angew Chem Int Ed Engl 2021; 60:17131-17137. [PMID: 34008286 DOI: 10.1002/anie.202105383] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 04/20/2021] [Indexed: 12/28/2022]
Abstract
Targeted covalent inhibitors have re-emerged as validated drugs to overcome acquired resistance in cancer treatment. Herein, by using a carbonyl boronic acid (CBA) warhead, we report the structure-based design of BCR-ABL inhibitors via reversible covalent targeting of the catalytic lysine with improved potency against both wild-type and mutant ABL kinases, especially ABLT315I bearing the gatekeeper residue mutation. We show the evolutionarily conserved lysine can be targeted selectively, and the selectivity depends largely on molecular recognition of the non-covalent pharmacophore in this class of inhibitors, probably due to the moderate reactivity of the warhead. We report the first co-crystal structures of covalent inhibitor-ABL kinase domain complexes, providing insights into the interaction of this warhead with the catalytic lysine. We also employed label-free mass spectrometry to evaluate off-targets of our compounds at proteome-wide level in different mammalian cells.
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Affiliation(s)
- David Quach
- NUS Graduate School for Integrative Sciences and Engineering, 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02, Singapore, 119077, Singapore.,Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Jothi Anantharajan
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - John L K Wee
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Priya Retna
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Rong Li
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Boping Liu
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Doris H Y Tee
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Perlyn Z Kwek
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Joma K Joy
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Wan-Qi Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Klement Foo
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Thomas H Keller
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Shao Q Yao
- NUS Graduate School for Integrative Sciences and Engineering, 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02, Singapore, 119077, Singapore.,Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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6
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Abstract
Traditionally small molecules have mainly been used to inhibit biochemical activities of proteins, however such compounds can also be used to change the conformational energy landscape of proteins. Tool compounds that modulate protein conformations often reveal unexpected biological mechanisms, which have therapeutic potential. We discuss two examples where screening hits were found to bind to unexpected binding pockets on well known proteins, establishing new routes for the inhibition of proteins that were thought to be undruggable.
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Affiliation(s)
- Congbao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, 138670, Singapore
| | - Thomas H Keller
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, 138670, Singapore.
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7
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Kwiatkowski J, Liu B, Pang S, Ahmad NHB, Wang G, Poulsen A, Yang H, Poh YR, Tee DHY, Ong E, Retna P, Dinie N, Kwek P, Wee JLK, Manoharan V, Low CB, Seah PG, Pendharkar V, Sangthongpitag K, Joy J, Baburajendran N, Jansson AE, Nacro K, Hill J, Keller TH, Hung AW. Stepwise Evolution of Fragment Hits against MAPK Interacting Kinases 1 and 2. J Med Chem 2020; 63:621-637. [DOI: 10.1021/acs.jmedchem.9b01582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jacek Kwiatkowski
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Boping Liu
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Shermaine Pang
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Nur Huda Binte Ahmad
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Gang Wang
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Haiyan Yang
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Yong Rui Poh
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Doris Hui Ying Tee
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Esther Ong
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Priya Retna
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Nurul Dinie
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Perlyn Kwek
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - John Liang Kuan Wee
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Vithya Manoharan
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Choon Bing Low
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Peck Gee Seah
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Vishal Pendharkar
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Kanda Sangthongpitag
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Joma Joy
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Anna Elisabet Jansson
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Kassoum Nacro
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Jeffrey Hill
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Thomas H. Keller
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
| | - Alvin W. Hung
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Way, Chromos #05-01/06, 138670 Singapore
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8
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Huang C, Liew SS, Lin GR, Poulsen A, Ang MJY, Chia BCS, Chew SY, Kwek ZP, Wee JLK, Ong EH, Retna P, Baburajendran N, Li R, Yu W, Koh-Stenta X, Ngo A, Manesh S, Fulwood J, Ke Z, Chung HH, Sepramaniam S, Chew XH, Dinie N, Lee MA, Chew YS, Low CB, Pendharkar V, Manoharan V, Vuddagiri S, Sangthongpitag K, Joy J, Matter A, Hill J, Keller TH, Foo K. Correction to "Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3". ACS Med Chem Lett 2019; 10:1240. [PMID: 31413812 DOI: 10.1021/acsmedchemlett.9b00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
[This corrects the article DOI: 10.1021/acsmedchemlett.9b00170.].
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9
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Baburajendran N, Kwiatkowski J, Liu B, Tee DHY, Keller TH, Hung AW, Hill J. Co-crystal structure of Protein kinase C-iota with inhibitor reveals a unique binding mode. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319099471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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10
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Anantharajan J, Zhou H, Zhang L, Hotz T, Vincent MY, Blevins MA, Jansson AE, Kuan JWL, Ng EY, Yeo YK, Baburajendran N, Lin G, Hung AW, Joy J, Patnaik S, Marugan J, Rudra P, Ghosh D, Hill J, Keller TH, Zhao R, Ford HL, Kang C. Structural and Functional Analyses of an Allosteric EYA2 Phosphatase Inhibitor That Has On-Target Effects in Human Lung Cancer Cells. Mol Cancer Ther 2019; 18:1484-1496. [PMID: 31285279 DOI: 10.1158/1535-7163.mct-18-1239] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 05/05/2019] [Accepted: 06/28/2019] [Indexed: 12/23/2022]
Abstract
EYA proteins (EYA1-4) are critical developmental transcriptional cofactors that contain an EYA domain (ED) harboring Tyr phosphatase activity. EYA proteins are largely downregulated after embryogenesis but are reexpressed in cancers, and their Tyr phosphatase activity plays an important role in the DNA damage response and tumor progression. We previously identified a class of small-molecule allosteric inhibitors that specifically inhibit the Tyr phosphatase activity of EYA2. Herein, we determined the crystal structure of the EYA2 ED in complex with NCGC00249987 (a representative compound in this class), revealing that it binds to an induced pocket distant from the active site. NCGC00249987 binding leads to a conformational change of the active site that is unfavorable for Mg2+ binding, thereby inhibiting EYA2's Tyr phosphatase activity. We demonstrate, using genetic mutations, that migration, invadopodia formation, and invasion of lung adenocarcinoma cells are dependent on EYA2 Tyr phosphatase activity, whereas growth and survival are not. Further, we demonstrate that NCGC00249987 specifically targets migration, invadopodia formation, and invasion of lung cancer cells, but that it does not inhibit cell growth or survival. The compound has no effect on lung cancer cells carrying an EYA2 F290Y mutant that abolishes compound binding, indicating that NCGC00249987 is on target in lung cancer cells. These data suggest that the NCGC00249987 allosteric inhibitor can be used as a chemical probe to study the function of the EYA2 Tyr phosphatase activity in cells and may have the potential to be developed into an antimetastatic agent for cancers reliant on EYA2's Tyr phosphatase activity.
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Affiliation(s)
| | - Hengbo Zhou
- Department of Pharmacology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Taylor Hotz
- Department of Pharmacology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Melanie Y Vincent
- Department of Pharmacology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Melanie A Blevins
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Anna E Jansson
- Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore
| | | | | | - Yee Khoon Yeo
- Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore
| | | | - Grace Lin
- Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore
| | - Alvin W Hung
- Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore
| | - Joma Joy
- Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore
| | - Samarjit Patnaik
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Juan Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Pratyaydipta Rudra
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jeffrey Hill
- Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore.
| | - Thomas H Keller
- Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore.
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado.
| | - Heide L Ford
- Department of Pharmacology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado. .,Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - CongBao Kang
- Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore.
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11
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Huang C, Liew SS, Lin GR, Poulsen A, Ang MJY, Chia BCS, Chew SY, Kwek ZP, Wee JLK, Ong EH, Retna P, Baburajendran N, Li R, Yu W, Koh-Stenta X, Ngo A, Manesh S, Fulwood J, Ke Z, Chung HH, Sepramaniam S, Chew XH, Dinie N, Lee MA, Chew YS, Low CB, Pendharkar V, Manoharan V, Vuddagiri S, Sangthongpitag K, Joy J, Matter A, Hill J, Keller TH, Foo K. Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3. ACS Med Chem Lett 2019; 10:978-984. [PMID: 31223458 DOI: 10.1021/acsmedchemlett.9b00170] [Citation(s) in RCA: 15] [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: 04/15/2019] [Accepted: 05/23/2019] [Indexed: 11/28/2022] Open
Abstract
SMYD3 is a histone methyltransferase that regulates gene transcription, and its overexpression is associated with multiple human cancers. A novel class of tetrahydroacridine compounds which inhibit SMYD3 through a covalent mechanism of action is identified. Optimization of these irreversible inhibitors resulted in the discovery of 4-chloroquinolines, a new class of covalent warheads. Tool compound 29 exhibits high potency by inhibiting SMYD3's enzymatic activity and showing antiproliferative activity against HepG2 in 3D cell culture. Our findings suggest that covalent inhibition of SMYD3 may have an impact on SMYD3 biology by affecting expression levels, and this warrants further exploration.
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Affiliation(s)
- Chuhui Huang
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Si Si Liew
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Grace R. Lin
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Anders Poulsen
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Melgious J. Y. Ang
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Brian C. S. Chia
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Sin Yin Chew
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Zekui P. Kwek
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - John L. K. Wee
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Esther H. Ong
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Priya Retna
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Nithya Baburajendran
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Rong Li
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Weixuan Yu
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Xiaoying Koh-Stenta
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Anna Ngo
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Sravanthy Manesh
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Justina Fulwood
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Zhiyuan Ke
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Hwa Hwa Chung
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | | | - Xin Hui Chew
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Nurul Dinie
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - May Ann Lee
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Yun Shan Chew
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Choon Bing Low
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Vishal Pendharkar
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Vithya Manoharan
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Susmitha Vuddagiri
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Kanda Sangthongpitag
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Joma Joy
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Alex Matter
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Jeffrey Hill
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Thomas H. Keller
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Klement Foo
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
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12
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Kwiatkowski J, Baburajendran N, Poulsen A, Liu B, Tee DHY, Wong YX, Poh ZY, Ong EHQ, Dinie N, Cherian J, Jansson AE, Hill J, Keller TH, Hung AW. Fragment-based Discovery of a Small-Molecule Protein Kinase C-iota Inhibitor Binding Post-kinase Domain Residues. ACS Med Chem Lett 2019; 10:318-323. [PMID: 30891133 DOI: 10.1021/acsmedchemlett.8b00546] [Citation(s) in RCA: 4] [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] [Received: 11/12/2018] [Accepted: 02/15/2019] [Indexed: 02/02/2023] Open
Abstract
The atypical protein kinase C-iota (PKC-ι) enzyme is implicated in various cancers and has been put forward as an attractive target for developing anticancer therapy. A high concentration biochemical screen identified pyridine fragment weakly inhibiting PKC-ι with IC50 = 424 μM. Driven by structure-activity relationships and guided by docking hypothesis, the weakly bound fragment was eventually optimized into a potent inhibitor of PKC-ι (IC50= 270 nM). Through the course of the optimization, an intermediate compound was crystallized with the protein, and careful analysis of the X-ray crystal structure revealed a unique binding mode involving the post-kinase domain (C-terminal tail) of PKC-ι.
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Affiliation(s)
- Jacek Kwiatkowski
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Nithya Baburajendran
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Anders Poulsen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Boping Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Doris Hui Ying Tee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Esther HQ Ong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Nurul Dinie
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Anna Elisabet Jansson
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Thomas H. Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
| | - Alvin W. Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore
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13
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Kwiatkowski J, Liu B, Tee DHY, Chen G, Ahmad NHB, Wong YX, Poh ZY, Ang SH, Tan ESW, Ong EH, Nurul Dinie, Poulsen A, Pendharkar V, Sangthongpitag K, Lee MA, Sepramaniam S, Ho SY, Cherian J, Hill J, Keller TH, Hung AW. Fragment-Based Drug Discovery of Potent Protein Kinase C Iota Inhibitors. J Med Chem 2018; 61:4386-4396. [PMID: 29688013 DOI: 10.1021/acs.jmedchem.8b00060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein kinase C iota (PKC-ι) is an atypical kinase implicated in the promotion of different cancer types. A biochemical screen of a fragment library has identified several hits from which an azaindole-based scaffold was chosen for optimization. Driven by a structure-activity relationship and supported by molecular modeling, a weakly bound fragment was systematically grown into a potent and selective inhibitor against PKC-ι.
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Affiliation(s)
- Jacek Kwiatkowski
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Boping Liu
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Doris Hui Ying Tee
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Guoying Chen
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Nur Huda Binte Ahmad
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Shi Hua Ang
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Eldwin Sum Wai Tan
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Esther Hq Ong
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Nurul Dinie
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Anders Poulsen
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Vishal Pendharkar
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Kanda Sangthongpitag
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - May Ann Lee
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Sugunavathi Sepramaniam
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Soo Yei Ho
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre , Agency for Science, Technology and Research (A*STAR) , 11 Biopolis Way, Helios #03-10/11 , Singapore 138667 , Singapore
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14
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Li Y, Ng HQ, Ngo A, Liu S, Tan YW, Kwek PZ, Hung AW, Joy J, Hill J, Keller TH, Kang C. Backbone resonance assignments for the SET domain of human methyltransferase NSD3 in complex with its cofactor. Biomol NMR Assign 2017; 11:225-229. [PMID: 28808922 DOI: 10.1007/s12104-017-9753-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
NSD3 is a histone H3 methyltransferase that plays an important role in chromatin biology. A construct containing the methyltransferase domain encompassing residues Q1049-K1299 of human NSD3 was obtained and biochemical activity was demonstrated using histone as a substrate. Here we report the backbone HN, N, Cα, C', and side chain Cβ assignments of the construct in complex with S-adenosyl-L-methionine (SAM). Based on these assignments, secondary structures of NSD3/SAM complex in solution were determined.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Anna Ngo
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Shuang Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Yih Wan Tan
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Perlyn Zekui Kwek
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Joma Joy
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore.
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15
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Abstract
The recent outbreak of Zika virus (ZIKV) infection has caused global concern due to its link to severe damage to the brain development of foetuses and neuronal complications in adult patients. A worldwide research effort has been undertaken to identify effective and safe treatment and vaccination options. Among the proposed viral and host components, the viral NS2B-NS3 protease represents an attractive drug target due to its essential role in the virus life cycle. Here, we outline recent progress in studies on the Zika protease. Biochemical, biophysical, and structural studies on different protease constructs provide new insight into the structure and activity of the protease. The unlinked construct displays higher enzymatic activity and better mimics the native state of the enzyme and therefore is better suited for drug discovery. Furthermore, the structure of the free enzyme adopts a closed conformation and a preformed active site. The availability of a lead fragment hit and peptide inhibitors, as well as the attainability of soakable crystals, suggest that the unlinked construct is a promising tool for drug discovery.
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Affiliation(s)
- CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, 138669, Singapore.
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, 138669, Singapore.
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, 636921, Singapore.
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16
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Li Y, Zhang Z, Phoo WW, Loh YR, Wang W, Liu S, Chen MW, Hung AW, Keller TH, Luo D, Kang C. Structural Dynamics of Zika Virus NS2B-NS3 Protease Binding to Dipeptide Inhibitors. Structure 2017; 25:1242-1250.e3. [DOI: 10.1016/j.str.2017.06.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/13/2017] [Accepted: 06/08/2017] [Indexed: 01/13/2023]
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17
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Ho SY, Alam J, Jeyaraj DA, Wang W, Lin GR, Ang SH, Tan ESW, Lee MA, Ke Z, Madan B, Virshup DM, Ding LJ, Manoharan V, Chew YS, Low CB, Pendharkar V, Sangthongpitag K, Hill J, Keller TH, Poulsen A. Scaffold Hopping and Optimization of Maleimide Based Porcupine Inhibitors. J Med Chem 2017; 60:6678-6692. [PMID: 28671458 DOI: 10.1021/acs.jmedchem.7b00662] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Porcupine is an O-acyltransferase that regulates Wnt secretion. Inhibiting porcupine may block the Wnt pathway which is often dysregulated in various cancers. Consequently porcupine inhibitors are thought to be promising oncology therapeutics. A high throughput screen against porcupine revealed several potent hits that were confirmed to be Wnt pathway inhibitors in secondary assays. We developed a pharmacophore model and used the putative bioactive conformation of a xanthine inhibitor for scaffold hopping. The resulting maleimide scaffold was optimized to subnanomolar potency while retaining good physical druglike properties. A preclinical development candidate was selected for which extensive in vitro and in vivo profiling is reported.
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Affiliation(s)
- Soo Yei Ho
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Jenefer Alam
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | | | - Weiling Wang
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Grace Ruiting Lin
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Shi Hua Ang
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Eldwin Sum Wai Tan
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - May Ann Lee
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Zhiyuan Ke
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Babita Madan
- Duke-NUS Graduate Medical School Singapore , 8 College Road, 169857, Singapore
| | - David M Virshup
- Duke-NUS Graduate Medical School Singapore , 8 College Road, 169857, Singapore
| | - Li Jun Ding
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Vithya Manoharan
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Yun Shan Chew
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Choon Bing Low
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Vishal Pendharkar
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Kanda Sangthongpitag
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Anders Poulsen
- Experimental Therapeutics Centre , 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
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18
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Li Y, Phoo WW, Loh YR, Zhang Z, Ng EY, Wang W, Keller TH, Luo D, Kang C. Structural characterization of the linked NS2B-NS3 protease of Zika virus. FEBS Lett 2017; 591:2338-2347. [PMID: 28675775 DOI: 10.1002/1873-3468.12741] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 05/09/2017] [Revised: 06/16/2017] [Accepted: 06/29/2017] [Indexed: 01/23/2023]
Abstract
The Zika virus (ZIKV) NS2B-NS3 protease is an important drug target. The conventional flaviviral protease constructs used for structural studies contain the NS2B cofactor region linked to the NS3 protease domain via a glycine-rich flexible linker. Here, we examined the structural dynamics of this conventional Zika protease (gZiPro) using NMR spectroscopy. Although the glycine-rich linker in gZiPro does not alter the overall folding of the protease in solution, gZiPro is not homogenous in ion exchange chromatography. Compared to the unlinked protease construct, the artificial linker affects the chemical environment of many residues including H51 in the catalytic triad. Our study provides a direct comparison of ZIKV protease constructs with and without an artificial linker.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Wint Wint Phoo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ying Ru Loh
- Experimental Therapeutics Centre Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Zhenzhen Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Elizabeth Yihui Ng
- Experimental Therapeutics Centre Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Weiling Wang
- Experimental Therapeutics Centre Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre Agency for Science Technology and Research (A*STAR), Singapore, Singapore
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19
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Li Y, Wong YL, Ng FM, Liu B, Wong YX, Poh ZY, Liu S, Then SW, Lee MY, Ng HQ, Huang Q, Hung AW, Cherian J, Hill J, Keller TH, Kang C. Escherichia coli Topoisomerase IV E Subunit and an Inhibitor Binding Mode Revealed by NMR Spectroscopy. J Biol Chem 2016; 291:17743-53. [PMID: 27365392 PMCID: PMC5016168 DOI: 10.1074/jbc.m116.737429] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/29/2016] [Indexed: 11/06/2022] Open
Abstract
Bacterial topoisomerases are attractive antibacterial drug targets because of their importance in bacterial growth and low homology with other human topoisomerases. Structure-based drug design has been a proven approach of efficiently developing new antibiotics against these targets. Past studies have focused on developing lead compounds against the ATP binding pockets of both DNA gyrase and topoisomerase IV. A detailed understanding of the interactions between ligand and target in a solution state will provide valuable information for further developing drugs against topoisomerase IV targets. Here we describe a detailed characterization of a known potent inhibitor containing a 9H-pyrimido[4,5-b]indole scaffold against the N-terminal domain of the topoisomerase IV E subunit from Escherichia coli (eParE). Using a series of biophysical and biochemical experiments, it has been demonstrated that this inhibitor forms a tight complex with eParE. NMR studies revealed the exact protein residues responsible for inhibitor binding. Through comparative studies of two inhibitors of markedly varied potencies, it is hypothesized that gaining molecular interactions with residues in the α4 and residues close to the loop of β1-α2 and residues in the loop of β3-β4 might improve the inhibitor potency.
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Affiliation(s)
- Yan Li
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Ying Lei Wong
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Fui Mee Ng
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Boping Liu
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Yun Xuan Wong
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Zhi Ying Poh
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Shuang Liu
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Siew Wen Then
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Michelle Yueqi Lee
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Hui Qi Ng
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Qiwei Huang
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Alvin W Hung
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Joseph Cherian
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Jeffrey Hill
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Thomas H Keller
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - CongBao Kang
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
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20
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Cherian J, Nacro K, Poh ZY, Guo S, Ho MWT, Yang H, Lim S, Choong ML, Joy JK, Zekui PZ, Liu B, Ong EH, Pendharkar V, Ding L, Poulsen A, Lee MA, Sangthongpitag K, Chuah C, Ong TS, Hill J, Keller TH, Matter A. Abstract 2137: Discovery of dual MNK 1 and 2 and BCR-ABL kinase inhibitors for the treatment of blast crisis chronic myeloid leukemia. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2137] [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 Phase Chronic Myelogenous Leukemia (CP-CML) is well treated with tyrosine kinase inhibitors (TKI) through BCR-ABL kinase modulation. However, TKI are ineffective for late-stage or blast crisis (BC) CML in which phase, granulocyte macrophage progenitors (GMPs) have acquired the ability to function as leukemic stem cells (LSCs), and are thought to act as a reservoir for TKI resistance with poor prognosis. An effective BC-CML therapy will likely have to target the BC-LSC population to ensure long-term disease control.
Recent studies have shown the importance of the MAP kinase interacting serine/threonine kinase (MNK1/2)-eukaryotic translation initiation factor 4E (eIF4E) axis in sustaining BC-LSC self-renewal. Thus, a single agent which inhibits both BCR-ABL and MNK1/2 kinase simultaneously represents a rational approach to target BC-LSCs. Such an agent should be able to distinguish between normal hematopoietic stem cells (HSC) and LSCs.
Here, we report the discovery of a potential BC-CML therapy that relies on the inhibition of MNK1/2 and BCR-ABL kinases using a dual specific MNK/ABL inhibitor. We will also report the in vitro and in vivo biological data, pharmacokinetic properties, and biochemical characteristics of such compounds. These compounds are able to prevent eIF4E phosphorylation, thus selectively inhibiting the MNK-eIF4E-dependent self-renewal function of BC-LSCs as a single agent while leaving normal HSCs unscathed.
Citation Format: Joseph Cherian, Kassoum Nacro, Zhi Ying Poh, Samantha Guo, Melvyn Wai Tuck Ho, Haiyan Yang, Sharon Lim, Meng Ling Choong, Joma Kanikadu Joy, Perlyn Z. Zekui, Boping Liu, Esther Hongqian Ong, Vishal Pendharkar, Lijun Ding, Anders Poulsen, May Ann Lee, Kanda Sangthongpitag, Charles Chuah, Tiong S. Ong, Jeffrey Hill, Thomas H. Keller, Alex Matter. Discovery of dual MNK 1 and 2 and BCR-ABL kinase inhibitors for the treatment of blast crisis chronic myeloid leukemia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2137.
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Affiliation(s)
| | - Kassoum Nacro
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Zhi Ying Poh
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Samantha Guo
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - Haiyan Yang
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Sharon Lim
- 2Duke-NUS Graduate Medical School, Singapore, Singapore
| | | | | | | | - Boping Liu
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | | | - Lijun Ding
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - May Ann Lee
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - Charles Chuah
- 2Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Tiong S. Ong
- 2Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jeffrey Hill
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - Alex Matter
- 1Experimental Therapeutics Centre, Singapore, Singapore
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21
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Nacro K, Yang H, Ho MWT, Yeap YS, Chennamaneni LR, Ang SH, Tan ESW, Duraiswamy AJ, Lim S, Liu B, Ong EH, Choong ML, Tai SJ, Manoharan V, Pendharkar V, Ding L, Chew YS, Joy JK, Kuan JLW, Kwek PZ, Poulsen A, Lee MA, Sangthongpitag K, Chuah C, Ong TS, Hill J, Keller TH, Matter A. Abstract 2134: Rational design of selective MNK 1 and 2 kinase inhibitors for the treatment of blast crisis chronic myeloid leukemia patients. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2134] [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
The marketed BCR-ABL tyrosine kinase inhibitor (TKI), imatinib (Gleevec™) is a very successful targeted anti-cancer therapy. It has revolutionized the treatment of early stage or chronic phase (CP) chronic myeloid leukemia (CML). Unfortunately, a proportion of CP patients experience suboptimal responses to BCR-ABL TKIs, and progress to blast crisis (BC) stage of CML with poor survival rate. A potential cause of the resistance to TKI is the elevated level of phosphorylated eukaryotic initiation factor 4E (eIF4E), which has been found to be a consistent feature in patient-derived BC-CML samples. Importantly, both in vivo and in vitro studies have demonstrated that the MAP kinase-interacting serine/threonine-protein kinases 1 and 2 (MNK1/2) phosphorylate eIF4E on Ser209, and that the overexpression of eIF4E drives oncogenesis in a variety of cancers including BC-CML. Furthermore, several reports have indicated that eIF4E phosphorylation at Ser209, as well as eIF4E overexpression, is critical to tumor progression.
We found that a BC-CML cell line, K562, that expresses a serine to alanine phospho-mutant at position 209 of eIF4E, shows reduced ability to form tumors in mice compared to wildtype eIF4E. In addition, our recent work has demonstrated the importance of the MNK-eIF4E axis in activating BC leukemia stem cell (LSC) function (Lim et al., PNAS18; 110(25):E2298-307, 2013). These data highlight the critical importance of MNK1/2-dependent eIF4E phosphorylation in cancer progression and maintenance, and suggests that inhibition of MNK1/2 is an attractive therapeutic approach to treat BC-CML. Consequently, we set out to identify selective inhibitors of the MNK1/2 kinases to treat BC-CML patients.
Here, we report our hit finding strategy, as well as our hit to lead optimization process. Results describing structure activity relationships, pharmacokinetics properties, and biochemical characteristics of a highly specific MNK1/2 inhibitor, are presented. Our data demonstrate that drug-like molecules can be developed to potently and specifically inhibit the MNK kinases. We also show that simultaneous inhibition of MNK and BCR-ABL is effective at inhibiting BCR-ABL-driven growth and proliferation, as well as inhibiting the MNK-eIF4E-dependent self-renewal function of BC-LSCs. A combination of selective MNK and BCR-ABL inhibitors may provide clinical benefit to BC-CML patients.
Citation Format: Kassoum Nacro, Haiyan Yang, Melvyn Wai Tuck Ho, Yoon Sheng Yeap, Lohitha Rao Chennamaneni, Shi Hua Ang, Eldwin Sum Wai Tan, Athisayamani Jeyaraj Duraiswamy, Sharon Lim, Boping Liu, Esther Hongqian Ong, Meng Ling Choong, Shi Jing Tai, Vithya Manoharan, Vishal Pendharkar, Lijun Ding, Yun Shan Chew, Joma Kanikadu Joy, John LW Kuan, Perlyn Z. Kwek, Anders Poulsen, May Ann Lee, Kanda Sangthongpitag, Charles Chuah, Tiong S. Ong, Jeffrey Hill, Thomas H. Keller, Alex Matter. Rational design of selective MNK 1 and 2 kinase inhibitors for the treatment of blast crisis chronic myeloid leukemia patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2134.
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Affiliation(s)
- Kassoum Nacro
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Haiyan Yang
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | | | | | - Shi Hua Ang
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | | | - Sharon Lim
- 3Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Boping Liu
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | | | - Shi Jing Tai
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | | | - Lijun Ding
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Yun Shan Chew
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - John LW Kuan
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | | | - May Ann Lee
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - Charles Chuah
- 3Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Tiong S. Ong
- 3Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jeffrey Hill
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - Alex Matter
- 1Experimental Therapeutics Centre, Singapore, Singapore
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22
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Cherian J, Nacro K, Poh ZY, Guo S, Jeyaraj DA, Wong YX, Ho M, Yang HY, Joy JK, Kwek ZP, Liu B, Wee JLK, Ong EHQ, Choong ML, Poulsen A, Lee MA, Pendharkar V, Ding LJ, Manoharan V, Chew YS, Sangthongpitag K, Lim S, Ong ST, Hill J, Keller TH. Structure–Activity Relationship Studies of Mitogen Activated Protein Kinase Interacting Kinase (MNK) 1 and 2 and BCR-ABL1 Inhibitors Targeting Chronic Myeloid Leukemic Cells. J Med Chem 2016; 59:3063-78. [DOI: 10.1021/acs.jmedchem.5b01712] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Joseph Cherian
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Kassoum Nacro
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Samantha Guo
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | | | - Yun Xuan Wong
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Melvyn Ho
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Hai Yan Yang
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Joma Kanikadu Joy
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Zekui Perlyn Kwek
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Boping Liu
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | | | - Esther HQ Ong
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Meng Ling Choong
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Anders Poulsen
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - May Ann Lee
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Vishal Pendharkar
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Li Jun Ding
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Vithya Manoharan
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Yun Shan Chew
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | | | - Sharon Lim
- Duke-National University of Singapore (NUS) Graduate Medical School, 8 College Road, Singapore, Singapore 169857
| | - S. Tiong Ong
- Duke-National University of Singapore (NUS) Graduate Medical School, 8 College Road, Singapore, Singapore 169857
| | - Jeffrey Hill
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
| | - Thomas H. Keller
- Experimental Therapeutics Centre, 13 Biopolis Way, Nanos, Singapore 138669
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Madan B, Ke Z, Harmston N, Petretto E, Hill J, Keller TH, Lee MA, Matter A, Virshup DM. Abstract B13: ETC-159 is a novel PORCN inhibitor effective for treatment of Wnt-addicted genetically defined cancers. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.devbiolca15-b13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Pathologic expression of Wnts is found in cancers, fibrosis and other diseases, hence there is considerable interest in blocking Wnt signaling to achieve therapeutic benefit. Post-translational palmitoleation of Wnts at a highly conserved serine residue is essential for their secretion and function. We have pursued a strategy to block all Wnt-dependent pathways concomitantly using a small molecule inhibitor of the enzyme PORCN that is required for Wnt O-palmitoleation. As Wnt pathway inhibitors advance to clinical trials, the paucity of well-defined biomarkers makes it challenging to monitor response to therapeutics.
We have developed a novel PORCN inhibitor ETC-159, which has remarkable efficacy in pre-clinical models of RNF43-mutant pancreatic and ovarian cancers and RSPO3-translocation bearing colorectal cancer patient derived xenografts. ETC-159 reverses Wnt dependent pathology by promoting cellular differentiation. Consistent with the role of Wnt/β-catenin signaling in regulation of diverse cellular functions, RNA sequencing of these ETC-159 sensitive, Wnt driven cancers has revealed significant remodeling of the transcriptome on treatment with ETC-159 with a decrease of cell cycle, stem cell, and proliferation genes and an increase in differentiation markers. Our studies show that coordinate regulation of NOTUM and AXIN2 gene expression may be a useful predictor of sensitivity to PORCN inhibitors. NOTUM is a secreted protein and its levels in serum correlate with tumor growth. Notum has potential to be a pharmacodynamic biomarker that will reflect a response to PORCN and other Wnt pathway inhibitors.
Citation Format: Babita Madan, Zhiyuan Ke, Nathan Harmston, Enrico Petretto, Jeffrey Hill, Thomas H. Keller, May Ann Lee, Alex Matter, David M. Virshup. ETC-159 is a novel PORCN inhibitor effective for treatment of Wnt-addicted genetically defined cancers. [abstract]. In: Proceedings of the AACR Special Conference: Developmental Biology and Cancer; Nov 30-Dec 3, 2015; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(4_Suppl):Abstract nr B13.
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Affiliation(s)
- Babita Madan
- 1Duke-NUS Graduate Medical School, Singapore, Singapore,
| | - Zhiyuan Ke
- 2Experimental Therapeutics Centre, A*STAR, Biopolis, Singapore, Singapore
| | | | | | - Jeffrey Hill
- 2Experimental Therapeutics Centre, A*STAR, Biopolis, Singapore, Singapore
| | - Thomas H. Keller
- 2Experimental Therapeutics Centre, A*STAR, Biopolis, Singapore, Singapore
| | - May Ann Lee
- 2Experimental Therapeutics Centre, A*STAR, Biopolis, Singapore, Singapore
| | - Alex Matter
- 2Experimental Therapeutics Centre, A*STAR, Biopolis, Singapore, Singapore
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24
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Nilar SH, Lakshminarayana SB, Ma NL, Keller TH, Blasco F, Smith PW. Artificial Neural Network Analysis of Pharmacokinetic and Toxicity Properties of Lead Molecules for Dengue Fever, Tuberculosis and Malaria. Curr Comput Aided Drug Des 2016; 12:52-61. [PMID: 26777113 DOI: 10.2174/1573409912999160112113539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/27/2015] [Accepted: 12/15/2015] [Indexed: 11/22/2022]
Abstract
Poor pharmacokinetic and toxicity profiles are major reasons for the low rate of advancing lead drug candidates into efficacy studies. The In-silico prediction of primary pharmacokinetic and toxicity properties in the drug discovery and development process can be used as guidance in the design of candidates. In-silico parameters can also be used to choose suitable compounds for in-vivo testing thereby reducing the number of animals used in experiments. At the Novartis Institute for Tropical Diseases, a data set has been curated from in-house measurements in the disease areas of Dengue, Tuberculosis and Malaria. Volume of distribution, half-life, total in-vivo clearance, in-vitro human plasma protein binding and in-vivo oral bioavailability have been measured for molecules in the lead optimization stage in each of these three disease areas. Data for the inhibition of the hERG channel using the radio ligand binding dofetilide assay was determined for a set of 300 molecules in these therapeutic areas. Based on this data, Artificial Neural Networks were used to construct In-silico models for each of the properties listed above that can be used to prioritize candidates for lead optimization and to assist in selecting promising molecules for in-vivo pharmacokinetic studies.
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Abstract
Over the past decade, academic groups and pharmaceutical companies have uncovered several components and targets for intervention in the Wnt pathway. One approach is to block Wnt signalling through the use of orally bioavailable small molecules that prevent Wnt ligand secretion. In recent years, the membrane bound O-acyl transferase (MBOAT) porcupine (PORCN) has emerged as a molecular target of interest in the search for clinical options to treat Wnt-driven cancers. This review shall provide an overview of the reported small molecule inhibitors for PORCN and discuss the progress made in identifying human disease models that are responsive to PORCN inhibitors.
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Affiliation(s)
- Soo Yei Ho
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore 138669, Singapore.
| | - Thomas H Keller
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore 138669, Singapore
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26
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Li Y, Wong YL, Ng FM, Liu B, Wong YX, Poh ZY, Then SW, Lee MY, Ng HQ, Hung AW, Cherian J, Hill J, Keller TH, Kang C. Characterization of the interaction between Escherichia coli topoisomerase IV E subunit and an ATP competitive inhibitor. Biochem Biophys Res Commun 2015; 467:961-6. [PMID: 26471301 DOI: 10.1016/j.bbrc.2015.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
Abstract
Bacterial topoisomerase IV (ParE) is essential for DNA replication and serves as an attractive target for antibacterial drug development. The X-ray structure of the N-terminal 24 kDa ParE, responsible for ATP binding has been solved. Due to the accessibility of structural information of ParE, many potent ParE inhibitors have been discovered. In this study, a pyridylurea lead molecule against ParE of Escherichia coli (eParE) was characterized with a series of biochemical and biophysical techniques. More importantly, solution NMR analysis of compound binding to eParE provides better understanding of the molecular interactions between the inhibitor and eParE.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Boping Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Siew Wen Then
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore.
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27
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Ang MJY, Lau QY, Ng FM, Then SW, Poulsen A, Cheong YK, Ngoh ZX, Tan YW, Peng J, Keller TH, Hill J, Chu JJH, Chia CSB. Peptidomimetic ethyl propenoate covalent inhibitors of the enterovirus 71 3C protease: a P2-P4 study. J Enzyme Inhib Med Chem 2015; 31:332-9. [PMID: 25792507 DOI: 10.3109/14756366.2015.1018245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 02/02/2015] [Indexed: 12/15/2022] Open
Abstract
Enterovirus 71 (EV71) is a highly infectious pathogen primarily responsible for Hand, Foot, and Mouth Disease, particularly among children. Currently, no approved antiviral drug has been developed against this disease. The EV71 3C protease is deemed an attractive drug target due to its crucial role in viral polyprotein processing. Rupintrivir, a peptide-based inhibitor originally developed to target the human rhinovirus 3C protease, was found to inhibit the EV71 3C protease. In this communication, we report the inhibitory activities of 30 Rupintrivir analogs against the EV71 3C protease. The most potent inhibitor, containing a P2 ring-constrained phenylalanine analog (compound 9), was found to be two-fold more potent than Rupintrivir (IC50 value 3.4 ± 0.4 versus 7.3 ± 0.8 μM). Our findings suggest that employing geometrically constrained residues in peptide-based protease inhibitors can potentially enhance their inhibitory activities.
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Affiliation(s)
- Melgious J Y Ang
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Qiu Ying Lau
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Fui Mee Ng
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Siew Wen Then
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Anders Poulsen
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Yuen Kuen Cheong
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Zi Xian Ngoh
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Yong Wah Tan
- b Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) , Singapore , and
| | - Jianhe Peng
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Thomas H Keller
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Jeffrey Hill
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Justin J H Chu
- b Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) , Singapore , and
- c Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology , National University of Singapore , Singapore
| | - C S Brian Chia
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore
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28
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Press NJ, Taylor RJ, Fullerton JD, Tranter P, McCarthy C, Keller TH, Arnold N, Beer D, Brown L, Cheung R, Christie J, Denholm A, Haberthuer S, Hatto JDI, Keenan M, Mercer MK, Oakman H, Sahri H, Tuffnell AR, Tweed M, Trifilieff A. Discovery and Optimization of 4-(8-(3-Fluorophenyl)-1,7-naphthyridin-6-yl)transcyclohexanecarboxylic Acid, an Improved PDE4 Inhibitor for the Treatment of Chronic Obstructive Pulmonary Disease (COPD). J Med Chem 2015; 58:6747-52. [PMID: 26288344 DOI: 10.1021/acs.jmedchem.5b00902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Neil J. Press
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Roger J. Taylor
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Joseph D. Fullerton
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Pamela Tranter
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Clive McCarthy
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Thomas H. Keller
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Nicola Arnold
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - David Beer
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Lyndon Brown
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Robert Cheung
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Julie Christie
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Alastair Denholm
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Sandra Haberthuer
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Julia D. I. Hatto
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Mark Keenan
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Mark K. Mercer
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Helen Oakman
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Helene Sahri
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Andrew R. Tuffnell
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Morris Tweed
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Alexandre Trifilieff
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
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29
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Li Y, Wong YX, Poh ZY, Wong YL, Lee MY, Ng HQ, Liu B, Hung AW, Cherian J, Hill J, Keller TH, Kang C. NMR structural characterization of the N-terminal active domain of the gyrase B subunit from Pseudomonas aeruginosa and its complex with an inhibitor. FEBS Lett 2015; 589:2683-9. [PMID: 26272827 DOI: 10.1016/j.febslet.2015.07.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/08/2015] [Accepted: 07/26/2015] [Indexed: 01/18/2023]
Abstract
The N-terminal ATP binding domain of the DNA gyrase B subunit is a validated drug target for antibacterial drug discovery. Structural information for this domain (pGyrB) from Pseudomonas aeruginosa is still missing. In this study, the interaction between pGyrB and a bis-pyridylurea inhibitor was characterized using several biophysical methods. We further carried out structural analysis of pGyrB using NMR spectroscopy. The secondary structures of free and inhibitor bound pGyrB were obtained based on backbone chemical shift assignment. Chemical shift perturbation and NOE experiments demonstrated that the inhibitor binds to the ATP binding pocket. The results of this study will be helpful for drug development targeting P. aeruginosa.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Boping Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
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30
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Duraiswamy AJ, Lee MA, Madan B, Ang SH, Tan ESW, Cheong WWV, Ke Z, Pendharkar V, Ding LJ, Chew YS, Manoharan V, Sangthongpitag K, Alam J, Poulsen A, Ho SY, Virshup DM, Keller TH. Discovery and Optimization of a Porcupine Inhibitor. J Med Chem 2015; 58:5889-99. [PMID: 26110200 DOI: 10.1021/acs.jmedchem.5b00507] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Wnt proteins regulate various cellular functions and serve distinct roles in normal development throughout life. Wnt signaling is dysregulated in various diseases including cancers. Porcupine (PORCN) is a membrane-bound O-acyltransferase that palmitoleates the Wnts and hence is essential for their secretion and function. The inhibition of PORCN could serve as a therapeutic approach for the treatment of a number of Wnt-dependent cancers. Herein, we describe the identification of a Wnt secretion inhibitor from cellular high throughput screening. Classical SAR based cellular optimization provided us with a PORCN inhibitor with nanomolar activity and excellent bioavailability that demonstrated efficacy in a Wnt-driven murine tumor model. Finally, we also discovered that enantiomeric PORCN inhibitors show very different activity in our reporter assay, suggesting that such compounds may be useful for mode of action studies on the PORCN O-acyltransferase.
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Affiliation(s)
| | - May Ann Lee
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Babita Madan
- ‡Duke-NUS Graduate Medical School Singapore, 8 College Road, 169857, Singapore
| | - Shi Hua Ang
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Eldwin Sum Wai Tan
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Wei Wen Vivien Cheong
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Zhiyuan Ke
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Vishal Pendharkar
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Li Jun Ding
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Yun Shan Chew
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Vithya Manoharan
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Kanda Sangthongpitag
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Jenefer Alam
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Anders Poulsen
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - Soo Yei Ho
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
| | - David M Virshup
- ‡Duke-NUS Graduate Medical School Singapore, 8 College Road, 169857, Singapore
| | - Thomas H Keller
- †Experimental Therapeutics Centre, 31 Biopolis Way, No. 03-01 Nanos, 138669, Singapore
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31
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Chen GY, Ng FM, Tan YW, Poulsen A, Seetoh W, Lin G, Kang C, Then SW, Ahmad NH, Wong YL, Ng HQ, Chia CSB, Lau QY, Hill J, Hung AW, Keller TH. Application of Fragment-Based Drug Discovery against DNA Gyrase B. Chempluschem 2015; 80:1250-1254. [PMID: 31973307 DOI: 10.1002/cplu.201500197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 04/29/2015] [Indexed: 11/11/2022]
Abstract
Bacterial resistance to antibiotics remains a serious threat to global health. The gyrase B enzyme is a well-validated target for developing antibacterial drugs. Despite being an attractive target for antibiotic development, there are currently no gyrase B inhibitory drugs on the market. A fragment screen using 1,800 compounds identified 14 fragments that bind to Escherichia coli (E. coli) gyrase B. The detailed characterization of binding is described for all 14 fragments. With the aid of X-ray crystallography, modifications on a low-affinity fragment (KD =253 μM, IC50 =634 μM) has led to the development of a new class of potent phenyl aminopyrazole inhibitors against E. coli gyrase B (IC50 =160 nM). The study presented here combines the use of a set of biophysical techniques including differential scanning fluorimetry, nuclear magnetic resonance, isothermal titration calorimetry, and X-ray crystallography to methodically identify, quantify, and optimize fragments into new chemical leads.
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Affiliation(s)
- Guo-Ying Chen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Yih Wan Tan
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Anders Poulsen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Weiguang Seetoh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Grace Lin
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Siew Wen Then
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Nur Huda Ahmad
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - C S Brian Chia
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Qiu Ying Lau
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
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32
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Poulsen A, Ho SY, Wang W, Alam J, Jeyaraj DA, Ang SH, Tan ESW, Lin GR, Cheong VWW, Ke Z, Lee MA, Keller TH. Pharmacophore Model for Wnt/Porcupine Inhibitors and Its Use in Drug Design. J Chem Inf Model 2015; 55:1435-48. [PMID: 26024410 DOI: 10.1021/acs.jcim.5b00159] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Porcupine is a component of the Wnt pathway which regulates cell proliferation, migration, stem cell self-renewal, and differentiation. The Wnt pathway has been shown to be dysregulated in a variety of cancers. Porcupine is a membrane bound O-acyltransferase that palmitoylates Wnt. Inhibiting porcupine blocks the secretion of Wnt and effectively inhibits the Wnt pathway. Using high throughput screening, we have identified a number of novel porcupine inhibitors with diverse scaffolds. The pharmacophore requirements for our porcupine inhibitors were elucidated, and a pharmacophore model is proposed. Our compounds as well as all currently published porcupine inhibitors may be fitted to this model in low energy conformations with good superimposition of the pharmacophore elements. The model also explains the stereochemical requirements of our chiral porcupine inhibitors. The pharmacophore model was successfully used for designing 3 new series of porcupine inhibitors having a tricyclic xantine, a phtalimide, or a piperidine-maleimide scaffold.
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Affiliation(s)
- Anders Poulsen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Soo Yei Ho
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Weiling Wang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Jenefer Alam
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Duraiswamy A Jeyaraj
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Shi Hua Ang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Eldwin Sum Wai Tan
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Grace Ruiting Lin
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Vivien Wei Wen Cheong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Zhiyuan Ke
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - May Ann Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way, Nanos Level 3, Singapore 138669
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33
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Abstract
Even though a number of groups have identified peptidic inhibitors for DENV and WNV proteases, and several high throughput screening campaigns have been performed, the progress towards drug candidates has been very slow. This is in stark contrast to the related NS3/NS4A protease of HCV for which two peptidomimetic drugs were approved in 2011. In this review we will compare the NS3 proteases of the flaviviruses WNV and DENV with that of HCV, and answer the question whether the flavivirus proteases are inherently more challenging, or whether the lack of success is simply due to the limited resources that have so far been invested in these neglected disease targets.
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Affiliation(s)
| | | | - Thomas H Keller
- Experimental Therapeutics Center, 31 Biopolis Way, #03-01 Nanos, Singapore 138669.
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34
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Cherian J, Nacro K, Poh ZY, Guo S, Ho M, Yang H, Lim S, Choong ML, Ding JL, Joy JK, Kwek ZP, Liu B, Ong HE, Pendharkar V, Poulsen A, Lee MA, Sangthongpitag K, Chuah C, Ong TS, Hill J, Keller TH, Matter A. Abstract 948: Discovery of dual MNK 1 and 2 and BCR-ABL kinase inhibitors for the treatment of blast crisis chronic myeloid leukemia. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-948] [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
Although targeting the BCR-ABL kinase with tyrosine kinase inhibitors (TKI) is effective in chronic phase (CP) CML, targeting BCR-ABL alone is not sufficient to treat late-stage or blast crisis (BC) CML. In BC CML, granulocyte macrophage progenitors (GMPs) acquire the ability to function as leukemic stem cells (LSCs), and are thought to act as a reservoir for TKI resistance. While long-term remission in BC CML is possible with allogeneic stem cell transplantation, only a minority of patients are eligible for transplantation, and may experience high morbidity and mortality. Safe and effective BC CML therapy will likely have to target the BC LSC population to ensure long-term disease control.
Recent studies have shown the importance of the MAP kinase interacting serine/threonine kinase (MNK1/2)-eukaryotic translation initiation factor 4E (eIF4E) axis in sustaining BC LSC self renewal. Thus, a single agent which inhibits both BCR-ABL and MNK1/2 kinase simultaneously represents a rational approach to target BC LSCs. Such an agent should be able to distinguish between normal hematopoietic stem cells (HSC) and LSCs.
Here, we report the discovery, structure activity relationships, pharmacokinetic properties, and biochemical characteristics of dual MNK1/2 and BCR-ABL inhibitors, ETC-027 and ETC-219. These compounds are able to prevent eIF4E phosphorylation, BCR-ABL-driven growth and proliferation of BC CML cells, as well as inhibit the MNK-eIF4E-dependent self-renewal function of BC LSCs, while leaving normal HSCs untouched.
Citation Format: Joseph Cherian, Kassoum Nacro, Zhi Ying Poh, Samantha Guo, Melvyn Ho, Haiyan Yang, Sharon Lim, Meng Ling Choong, Jun Li Ding, Joma Kanikadu Joy, Zekui Perlyn Kwek, Boping Liu, Hongqian Esther Ong, Vishal Pendharkar, Anders Poulsen, May Ann Lee, Kanda Sangthongpitag, Charles Chuah, Tiong S. Ong, Jeffrey Hill, Thomas H. Keller, Alex Matter. Discovery of dual MNK 1 and 2 and BCR-ABL kinase inhibitors for the treatment of blast crisis chronic myeloid leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 948. doi:10.1158/1538-7445.AM2014-948
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Affiliation(s)
| | - Kassoum Nacro
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Zhi Ying Poh
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Samantha Guo
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Melvyn Ho
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Haiyan Yang
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | - Sharon Lim
- 2Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | | | - Jun L. Ding
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | | | - Boping Liu
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | | | | | - May Ann Lee
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - Charles Chuah
- 3Hematology, Singapore General Hospital, Singapore, Singapore
| | - Tiong S. Ong
- 2Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jeffrey Hill
- 1Experimental Therapeutics Centre, Singapore, Singapore
| | | | - Alex Matter
- 1Experimental Therapeutics Centre, Singapore, Singapore
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35
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Nilar SH, Ma NL, Keller TH. The importance of molecular complexity in the design of screening libraries. J Comput Aided Mol Des 2013; 27:783-92. [DOI: 10.1007/s10822-013-9683-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 10/07/2013] [Indexed: 01/20/2023]
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36
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Larsson EA, Jansson A, Ng FM, Then SW, Panicker R, Liu B, Sangthongpitag K, Pendharkar V, Tai SJ, Hill J, Dan C, Ho SY, Cheong WW, Poulsen A, Blanchard S, Lin GR, Alam J, Keller TH, Nordlund P. Fragment-based ligand design of novel potent inhibitors of tankyrases. J Med Chem 2013; 56:4497-508. [PMID: 23672613 DOI: 10.1021/jm400211f] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Tankyrases constitute potential drug targets for cancer and myelin-degrading diseases. We have applied a structure- and biophysics-driven fragment-based ligand design strategy to discover a novel family of potent inhibitors for human tankyrases. Biophysical screening based on a thermal shift assay identified highly efficient fragments binding in the nicotinamide-binding site, a local hot spot for fragment binding. Evolution of the fragment hit 4-methyl-1,2-dihydroquinolin-2-one (2) along its 7-vector yields dramatic affinity improvements in the first cycle of expansion. A crystal structure of 7-(2-fluorophenyl)-4-methylquinolin-2(1H)-one (11) reveals that the nonplanar compound extends with its fluorine atom into a pocket, which coincides with a region of the active site where structural differences are seen between tankyrases and other poly(ADP-ribose) polymerase (PARP) family members. A further cycle of optimization yielded compounds with affinities and IC50 values in the low nanomolar range and with good solubility, PARP selectivity, and ligand efficiency.
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Affiliation(s)
- E Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, Lab 07-01, 61 Biopolis Drive (Proteos), Singapore 138673.
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Kim YM, Gayen S, Kang C, Joy J, Huang Q, Chen AS, Wee JLK, Ang MJY, Lim HA, Hung AW, Li R, Noble CG, Lee LT, Yip A, Wang QY, Chia CSB, Hill J, Shi PY, Keller TH. NMR analysis of a novel enzymatically active unlinked dengue NS2B-NS3 protease complex. J Biol Chem 2013; 288:12891-900. [PMID: 23511634 DOI: 10.1074/jbc.m112.442723] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The dengue virus (DENV) is a mosquito-borne pathogen responsible for an estimated 100 million human infections annually. The viral genome encodes a two-component trypsin-like protease that contains the cofactor region from the nonstructural protein NS2B and the protease domain from NS3 (NS3pro). The NS2B-NS3pro complex plays a crucial role in viral maturation and has been identified as a potential drug target. Using a DENV protease construct containing NS2B covalently linked to NS3pro via a Gly4-Ser-Gly4 linker ("linked protease"), previous x-ray crystal structures show that the C-terminal fragment of NS2B is remote from NS3pro and exists in an open state in the absence of an inhibitor; however, in the presence of an inhibitor, NS2B complexes with NS3pro to form a closed state. This linked enzyme produced NMR spectra with severe signal overlap and line broadening. To obtain a protease construct with a resolved NMR spectrum, we expressed and purified an unlinked protease complex containing a 50-residue segment of the NS2B cofactor region and NS3pro without the glycine linker using a coexpression system. This unlinked protease complex was catalytically active at neutral pH in the absence of glycerol and produced dispersed cross-peaks in a (1)H-(15)N heteronuclear single quantum correlation spectrum that enabled us to conduct backbone assignments using conventional techniques. In addition, titration with an active-site peptide aldehyde inhibitor and paramagnetic relaxation enhancement studies demonstrated that the unlinked DENV protease exists predominantly in a closed conformation in solution. This protease complex can serve as a useful tool for drug discovery against DENV.
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Affiliation(s)
- Young Mee Kim
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore 138669
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38
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Kang C, Gayen S, Wang W, Severin R, Chen AS, Lim HA, Chia CSB, Schüller A, Doan DNP, Poulsen A, Hill J, Vasudevan SG, Keller TH. Exploring the binding of peptidic West Nile virus NS2B-NS3 protease inhibitors by NMR. Antiviral Res 2012; 97:137-44. [PMID: 23211132 DOI: 10.1016/j.antiviral.2012.11.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/23/2012] [Accepted: 11/24/2012] [Indexed: 11/26/2022]
Abstract
West Nile virus (WNV) NS2B-NS3 protease is an important drug target since it is an essential protein for the replication of the virus. In order to determine the minimum pharmacophore for protease inhibition, a series of dipeptide aldehydes were synthesized. The 50% inhibitory concentration (IC(50)) measurements revealed that a simple acetyl-KR-aldehyde was only threefold less active than 4-phenyl-phenylacetyl-KKR-aldehyde (1) (Stoermer et al., 2008) that was used as the reference compound. The ligand efficiency of 0.40 kcal/mol/HA (HA=heavy atom) for acetyl-KR-aldehyde is much improved compared to the reference compound 1 (0.23 kcal/mol/HA). The binding of the inhibitors was examined using (1)H-(15)N-HSQC experiments and differential chemical shifts were used to map the ligand binding sites. The biophysical studies show that the conformational mobility of WNV protease has a major impact on the design of novel inhibitors, since the protein conformation changes profoundly depending on the structure of the bound ligand.
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Affiliation(s)
- CongBao Kang
- Experimental Therapeutics Center, Nanos, Singapore, Singapore
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39
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Press NJ, Taylor RJ, Fullerton JD, Tranter P, McCarthy C, Keller TH, Arnold N, Beer D, Brown L, Cheung R, Christie J, Denholm A, Haberthuer S, Hatto JDI, Keenan M, Mercer MK, Oakman H, Sahri H, Tuffnell AR, Tweed M, Tyler JW, Wagner T, Fozard JR, Trifilieff A. Solubility-Driven Optimization of Phosphodiesterase-4 Inhibitors Leading to a Clinical Candidate. J Med Chem 2012; 55:7472-9. [PMID: 22889281 DOI: 10.1021/jm300459a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Neil J. Press
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham,
West Sussex RH12 5AB, U.K
| | - Roger J. Taylor
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham,
West Sussex RH12 5AB, U.K
| | | | - Pamela Tranter
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham,
West Sussex RH12 5AB, U.K
| | | | | | | | - David Beer
- Novartis Institute for Tropical Diseases, 10 Biopolis
Road, 05-01 Chromos, 138670 Singapore
| | | | | | | | | | | | - Julia D. I. Hatto
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham,
West Sussex RH12 5AB, U.K
| | | | | | - Helen Oakman
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham,
West Sussex RH12 5AB, U.K
| | | | | | | | - John W. Tyler
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham,
West Sussex RH12 5AB, U.K
| | - Trixie Wagner
- Novartis Institutes for Biomedical Research, Lichtstrasse 35, CH-4056
Basel, Switzerland
| | - John R. Fozard
- Novartis
Distinguished Scientist, Novartis Institutes for Biomedical Research,
Lichtstrasse 35, CH-4056 Basel, Switzerland
| | - Alexandre Trifilieff
- Novartis Institutes for Biomedical Research, Lichtstrasse 35, CH-4056
Basel, Switzerland
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40
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Zou B, Yap P, Sonntag LS, Leong SY, Yeung BKS, Keller TH. Mechanistic study of the spiroindolones: a new class of antimalarials. Molecules 2012; 17:10131-41. [PMID: 22922283 PMCID: PMC6268731 DOI: 10.3390/molecules170910131] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [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: 07/04/2012] [Revised: 08/11/2012] [Accepted: 08/16/2012] [Indexed: 11/16/2022] Open
Abstract
During the synthesis of the new antimalarial drug candidate NITD609, a high degree of diastereoselectivity was observed in the Pictet-Spengler reaction. By isolating both the 4E and 4Z imine intermediates, a systematic mechanistic study of the reaction under both kinetic and thermodynamic conditions was conducted. This study provides insight into the source of the diastereoselectivity for this important class of compounds.
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Affiliation(s)
- Bin Zou
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore
- Author to whom correspondence should be addressed; ; Tel.: +65-6722-2921; Fax: +65-6722-2918
| | - Peiling Yap
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore
| | | | - Seh Yong Leong
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore
| | - Bryan K. S. Yeung
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore
| | - Thomas H. Keller
- Experimental Therapeutics Centre, 31 Biopolis Drive, #03-01 Nanos, Singapore;
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Matter A, Keller TH. State of the art technologies in drug discovery 2011. Curr Opin Chem Biol 2011; 15:461-2. [DOI: 10.1016/j.cbpa.2011.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Cherian J, Choi I, Nayyar A, Manjunatha UH, Mukherjee T, Lee YS, Boshoff HI, Singh R, Ha YH, Goodwin M, Lakshminarayana SB, Niyomrattanakit P, Jiricek J, Ravindran S, Dick T, Keller TH, Dartois V, Barry CE. Structure-activity relationships of antitubercular nitroimidazoles. 3. Exploration of the linker and lipophilic tail of ((s)-2-nitro-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazin-6-yl)-(4-trifluoromethoxybenzyl)amine (6-amino PA-824). J Med Chem 2011; 54:5639-59. [PMID: 21755942 DOI: 10.1021/jm1010644] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The (S)-2-nitro-6-(4-(trifluoromethoxy)benzyloxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine named PA-824 (1) has demonstrated antitubercular activity in vitro and in animal models and is currently in clinical trials. We synthesized derivatives at three positions of the 4-(trifluoromethoxy)benzylamino tail, and these were tested for whole-cell activity against both replicating and nonreplicating Mycobacterium tuberculosis (Mtb). In addition, we determined their kinetic parameters as substrates of the deazaflavin-dependent nitroreductase (Ddn) from Mtb that reductively activates these pro-drugs. These studies yielded multiple compounds with 40 nM aerobic whole cell activity and 1.6 μM anaerobic whole cell activity: 10-fold improvements over both characteristics from the parent molecule. Some of these compounds exhibited enhanced solubility with acceptable stability to microsomal and in vivo metabolism. Analysis of the conformational preferences of these analogues using quantum chemistry suggests a preference for a pseudoequatorial orientation of the linker and lipophilic tail.
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Affiliation(s)
- Joseph Cherian
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, Singapore, 138670
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43
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Abstract
Indium-mediated allylation has been used in the site-selective functionalization of N-terminal aldehydes of peptides and proteins. This is the first demonstration of indium-mediated C-C bond formation in protein labelling studies under mild and environmentally friendly conditions.
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Affiliation(s)
- Jenefer Alam
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, 1 Nanyang Walk, Block 5 Level 3, Nanyang Technological University, Singapore 637371, Singapore
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44
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Lim SP, Sonntag LS, Noble C, Nilar SH, Ng RH, Zou G, Monaghan P, Chung KY, Dong H, Liu B, Bodenreider C, Lee G, Ding M, Chan WL, Wang G, Jian YL, Chao AT, Lescar J, Yin Z, Vedananda TR, Keller TH, Shi PY. Small molecule inhibitors that selectively block dengue virus methyltransferase. J Biol Chem 2011; 286:6233-40. [PMID: 21147775 PMCID: PMC3057852 DOI: 10.1074/jbc.m110.179184] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 11/23/2010] [Indexed: 01/16/2023] Open
Abstract
Crystal structure analysis of Flavivirus methyltransferases uncovered a flavivirus-conserved cavity located next to the binding site for its cofactor, S-adenosyl-methionine (SAM). Chemical derivatization of S-adenosyl-homocysteine (SAH), the product inhibitor of the methylation reaction, with substituents that extend into the identified cavity, generated inhibitors that showed improved and selective activity against dengue virus methyltransferase (MTase), but not related human enzymes. Crystal structure of dengue virus MTase with a bound SAH derivative revealed that its N6-substituent bound in this cavity and induced conformation changes in residues lining the pocket. These findings demonstrate that one of the major hurdles for the development of methyltransferase-based therapeutics, namely selectivity for disease-related methyltransferases, can be overcome.
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Affiliation(s)
- Siew Pheng Lim
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | | | - Christian Noble
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Shahul H. Nilar
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Ru Hui Ng
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Gang Zou
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Paul Monaghan
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Ka Yan Chung
- the School of Biological Sciences, Nanyang Technological University, Singapore, and
| | - Hongping Dong
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Boping Liu
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | | | - Gladys Lee
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Mei Ding
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Wai Ling Chan
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Gang Wang
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Yap Li Jian
- the School of Biological Sciences, Nanyang Technological University, Singapore, and
| | | | - Julien Lescar
- the School of Biological Sciences, Nanyang Technological University, Singapore, and
| | - Zheng Yin
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - T. R. Vedananda
- the Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139
| | - Thomas H. Keller
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Pei-Yong Shi
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
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45
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Abstract
The scope of the catalyst-free water-based Mukaiyama aldol reaction was explored through its application to the site-selective functionalization of N-terminal aldehydes of peptides and proteins. Various functional groups were introduced under mild and environmentally friendly conditions, with the first demonstration of aldol C-C bond formation in protein labeling studies. The efficiency and speed achieved in protein labeling can be of special interest in chemical biology studies.
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Affiliation(s)
- Jenefer Alam
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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46
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Rottmann M, McNamara C, Yeung BKS, Lee MCS, Zou B, Russell B, Seitz P, Plouffe DM, Dharia NV, Tan J, Cohen SB, Spencer KR, González-Páez GE, Lakshminarayana SB, Goh A, Suwanarusk R, Jegla T, Schmitt EK, Beck HP, Brun R, Nosten F, Renia L, Dartois V, Keller TH, Fidock DA, Winzeler EA, Diagana TT. Spiroindolones, a potent compound class for the treatment of malaria. Science 2010; 329:1175-80. [PMID: 20813948 DOI: 10.1126/science.1193225] [Citation(s) in RCA: 902] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Recent reports of increased tolerance to artemisinin derivatives--the most recently adopted class of antimalarials--have prompted a need for new treatments. The spirotetrahydro-beta-carbolines, or spiroindolones, are potent drugs that kill the blood stages of Plasmodium falciparum and Plasmodium vivax clinical isolates at low nanomolar concentration. Spiroindolones rapidly inhibit protein synthesis in P. falciparum, an effect that is ablated in parasites bearing nonsynonymous mutations in the gene encoding the P-type cation-transporter ATPase4 (PfATP4). The optimized spiroindolone NITD609 shows pharmacokinetic properties compatible with once-daily oral dosing and has single-dose efficacy in a rodent malaria model.
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Affiliation(s)
- Matthias Rottmann
- Swiss Tropical and Public Health Institute, Parasite Chemotherapy, CH-4002 Basel, Switzerland
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47
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Yeung BKS, Zou B, Rottmann M, Lakshminarayana SB, Ang SH, Leong SY, Tan J, Wong J, Keller-Maerki S, Fischli C, Goh A, Schmitt EK, Krastel P, Francotte E, Kuhen K, Plouffe D, Henson K, Wagner T, Winzeler EA, Petersen F, Brun R, Dartois V, Diagana TT, Keller TH. Spirotetrahydro beta-carbolines (spiroindolones): a new class of potent and orally efficacious compounds for the treatment of malaria. J Med Chem 2010; 53:5155-64. [PMID: 20568778 PMCID: PMC6996867 DOI: 10.1021/jm100410f] [Citation(s) in RCA: 318] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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The antiplasmodial activity of a series of spirotetrahydro β-carbolines is described. Racemic spiroazepineindole (1) was identified from a phenotypic screen on wild type Plasmodium falciparum with an in vitro IC50 of 90 nM. Structure−activity relationships for the optimization of 1 to compound 20a (IC50 = 0.2 nM) including the identification of the active 1R,3S enantiomer and elimination of metabolic liabilities is presented. Improvement of the pharmacokinetic profile of the series translated to exceptional oral efficacy in the P. berghei infected malaria mouse model where full cure was achieved in four of five mice with three daily doses of 30 mg/kg.
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Affiliation(s)
- Bryan K S Yeung
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01 Chromos, Singapore 138670.
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48
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Pethe K, Sequeira PC, Agarwalla S, Rhee K, Kuhen K, Phong WY, Patel V, Beer D, Walker JR, Duraiswamy J, Jiricek J, Keller TH, Chatterjee A, Tan MP, Ujjini M, Rao SPS, Camacho L, Bifani P, Mak PA, Ma I, Barnes SW, Chen Z, Plouffe D, Thayalan P, Ng SH, Au M, Lee BH, Tan BH, Ravindran S, Nanjundappa M, Lin X, Goh A, Lakshminarayana SB, Shoen C, Cynamon M, Kreiswirth B, Dartois V, Peters EC, Glynne R, Brenner S, Dick T. A chemical genetic screen in Mycobacterium tuberculosis identifies carbon-source-dependent growth inhibitors devoid of in vivo efficacy. Nat Commun 2010; 1:57. [PMID: 20975714 PMCID: PMC3220188 DOI: 10.1038/ncomms1060] [Citation(s) in RCA: 211] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 07/29/2010] [Indexed: 11/29/2022] Open
Abstract
Candidate antibacterials are usually identified on the basis of their in vitro activity. However, the apparent inhibitory activity of new leads can be misleading because most culture media do not reproduce an environment relevant to infection in vivo. In this study, while screening for novel anti-tuberculars, we uncovered how carbon metabolism can affect antimicrobial activity. Novel pyrimidine–imidazoles (PIs) were identified in a whole-cell screen against Mycobacterium tuberculosis. Lead optimization generated in vitro potent derivatives with desirable pharmacokinetic properties, yet without in vivo efficacy. Mechanism of action studies linked the PI activity to glycerol metabolism, which is not relevant for M. tuberculosis during infection. PIs induced self-poisoning of M. tuberculosis by promoting the accumulation of glycerol phosphate and rapid ATP depletion. This study underlines the importance of understanding central bacterial metabolism in vivo and of developing predictive in vitro culture conditions as a prerequisite for the rational discovery of new antibiotics. Candidate anti-tuberculosis drugs are often identified in whole-cell screens. Here, Pethe et al. show that inappropriate carbon-source selection can lead to the identification of compounds devoid of efficacy in vivo, underlining the importance of developing predictive in vitro screens.
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Affiliation(s)
- Kevin Pethe
- Novartis Institute for Tropical Diseases, #05-01 Chromos, Singapore 138670, Singapore.
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49
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Kim P, Kang S, Boshoff HI, Jiricek J, Collins M, Singh R, Manjunatha UH, Niyomrattanakit P, Zhang L, Goodwin M, Dick T, Keller TH, Dowd CS, Barry CE. Structure-activity relationships of antitubercular nitroimidazoles. 2. Determinants of aerobic activity and quantitative structure-activity relationships. J Med Chem 2010; 52:1329-44. [PMID: 19209893 DOI: 10.1021/jm801374t] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The (S)-2-nitro-6-substituted 6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazines have been extensively explored for their potential use as new antituberculars based on their excellent bactericidal properties on aerobic whole cells of Mycobacterium tuberculosis. An oxygen atom at the 2-position of the imidazole ring is required for aerobic activity. Here, we show that substitution of this oxygen by either nitrogen or sulfur yielded equipotent analogues. Acylating the amino series, oxidizing the thioether, or replacing the ether oxygen with carbon significantly reduced the potency of the compounds. Replacement of the benzylic oxygen at the 6-position by nitrogen slightly improved potency and facilitated exploration of the SAR in the more soluble 6-amino series. Significant improvements in potency were realized by extending the linker region between the 6-(S) position and the terminal hydrophobic aromatic substituent. A simple four-feature QSAR model was derived to rationalize MIC results in this series of bicyclic nitroimidazoles.
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Affiliation(s)
- Pilho Kim
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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50
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Kim P, Zhang L, Manjunatha UH, Singh R, Patel S, Jiricek J, Keller TH, Boshoff HI, Barry CE, Dowd CS. Structure-activity relationships of antitubercular nitroimidazoles. 1. Structural features associated with aerobic and anaerobic activities of 4- and 5-nitroimidazoles. J Med Chem 2010; 52:1317-28. [PMID: 19209889 DOI: 10.1021/jm801246z] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 4-nitroimidazole PA-824 is active against aerobic and anaerobic Mycobacterium tuberculosis (Mtb) while 5-nitroimidazoles like metronidazole are active against only anaerobic Mtb. We have synthesized analogues of both 4- and 5-nitroimidazoles and explored their antitubercular activities. The nitro group is required for both activities in all compounds. The key determinants of aerobic activity in the 4-nitroimidazoles include the bicyclic oxazine, the lipophilic tail, and the 2-position oxygen. For the 5-nitroimidazoles, neither the corresponding bicyclic analogue nor addition of a lipophilic tail conveyed aerobic activity. Incorporation of a 2-position oxygen atom into a rigid 5-nitroimidazooxazine provided the first 5-nitroimidazole with aerobic activity. Across both series, anaerobic and aerobic activities were not correlated and Mtb mutants lacking the deazaflavin-dependent nitroreductase (Ddn) retained anaerobic sensitivity to some compounds. Aerobic activity appears to be correlated with efficiency as a substrate for Ddn, suggesting a means of structure-based optimization of improved nitroimidazoles.
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Affiliation(s)
- Pilho Kim
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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