1
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Jones LH. Synthetic modification of protein surfaces to mediate induced-proximity pharmacology. RSC Med Chem 2024:d4md00388h. [PMID: 39185450 PMCID: PMC11342125 DOI: 10.1039/d4md00388h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024] Open
Abstract
Molecular glues and bifunctional small molecules, such as targeted protein degraders, induce protein proximity to mediate gain-of-function pharmacology. Emerging technologies that synthetically manipulate protein surfaces to create neoproteins, and the development of covalent chemical probes for intra- and inter-protein surface labeling are described. Ligand-directed protein surface modification strategies have the potential to enhance the induced-proximity pharmacology toolkit and expand the druggable proteome, and this Opinion considers the opportunities and challenges that lie ahead.
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Affiliation(s)
- Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute 360 Longwood Avenue Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA USA
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2
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Leu JH, Miao X, Shalayda K, Coe KJ, Kahnt A, Wu B, Schnarr M, Franks C, Devlin J, Yang TY, Palmer JA, Zhang M, Zhou H, Van Damme W, Smets S, Aguilar Z, Chaplan SR. A Phase 1 First-in-Human Pharmacokinetic and Pharmacodynamic Study of JNJ-64264681, a Covalent Inhibitor of Bruton's Tyrosine Kinase. Clin Pharmacol Drug Dev 2023; 12:611-624. [PMID: 37125450 DOI: 10.1002/cpdd.1253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/06/2023] [Indexed: 05/02/2023]
Abstract
JNJ-64264681 is an irreversible covalent inhibitor of Bruton's tyrosine kinase. This phase 1, first-in-human, 2-part (single-ascending dose [SAD]; multiple-ascending dose [MAD]) study evaluated the safety, tolerability, pharmacokinetics (PK), and pharmacodynamics (PD; Bruton's tyrosine kinase occupancy [BTKO]) of JNJ-64264681 oral solution in healthy participants. For SAD (N = 78), 6 increasing doses of JNJ-64264681 (4-400 mg) or placebo were evaluated in fasted males. The effects of sex, food, and a capsule formulation were evaluated in separate cohorts. For MAD (N = 27), sequential cohorts of male and female participants received 36/100/200 mg JNJ-64264681 once daily for 10 days. JNJ-64264681 exposure (peak concentration; area under the concentration-time curve) was less than dose proportional from 4 mg to 36 mg. Dose-normalized area under the concentration-time curves following the 36 mg and 100 mg doses were generally similar. The mean terminal half-life was 1.6-13.2 hours. With multiple doses, steady state was achieved by day 2. A semimechanistic PK/PD model was developed using the first 5 SAD cohorts' data to predict %BTKO in MAD cohorts. PK/PD model guided dose-escalation, and all participants in the 200/400 mg single-dose cohorts achieved ≥90% BTKO at 4 hours after dosing (peak) with prolonged occupancy. As BTKO data became available from MAD cohorts, it was found that observed BTKO data were consistent with model predictions. JNJ-64264681 showed no safety signals of concern. Overall, safety, tolerability, PK, BTKO, and PK/PD modeling guided the rationale for dose selection for the subsequent first-in-patient lymphoma studies.
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Affiliation(s)
- Jocelyn H Leu
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Xin Miao
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Kevin Shalayda
- Janssen Research & Development, LLC, Raritan, New Jersey, USA
| | - Kevin J Coe
- Janssen Research & Development, LLC, San Diego, California, USA
| | | | - Bonnie Wu
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Megan Schnarr
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Carol Franks
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - James Devlin
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Tong-Yuan Yang
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - James A Palmer
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Mai Zhang
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Honghui Zhou
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
- Present affiliation: Kira Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Wim Van Damme
- Clinical Pharmacology Unit, Janssen Research & Development, Merksem, Belgium
| | - Sophie Smets
- Clinical Pharmacology Unit, Janssen Research & Development, Merksem, Belgium
| | - Zuleima Aguilar
- Janssen Research & Development, LLC, San Diego, California, USA
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3
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Centrosome Defects in Hematological Malignancies: Molecular Mechanisms and Therapeutic Insights. BLOOD SCIENCE 2022; 4:143-151. [DOI: 10.1097/bs9.0000000000000127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
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4
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Su R, Diao Y, Sha W, Dou D, Yu Z, Leng L, Zhao Z, Chen Z, Li H, Xu Y. Discovery of pyrrolo[1,2-a]quinoxalin-4(5H)-one Derivatives as Novel Non-covalent Bruton’s Tyrosine Kinase (BTK) inhibitors. Bioorg Chem 2022; 126:105860. [DOI: 10.1016/j.bioorg.2022.105860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/02/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
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5
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Dou D, Diao Y, Sha W, Su R, Tong L, Li W, Leng L, Xie L, Yu Z, Song H, Shen Z, Zhu L, Zhao Z, Xie H, Chen Z, Li H, Xu Y. Discovery of Pteridine-7(8 H)-one Derivatives as Potent and Selective Inhibitors of Bruton's Tyrosine Kinase (BTK). J Med Chem 2022; 65:2694-2709. [PMID: 35099969 DOI: 10.1021/acs.jmedchem.1c02208] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Bruton's tyrosine kinase (BTK) is an attractive therapeutic target in the treatment of cancer, inflammation, and autoimmune diseases. Covalent and noncovalent BTK inhibitors have been developed, among which covalent BTK inhibitors have shown great clinical efficacy. However, some of them could produce adverse effects, such as diarrhea, rash, and platelet dysfunction, which are associated with the off-target inhibition of ITK and EGFR. In this study, we disclosed a series of pteridine-7(8H)-one derivatives as potent and selective covalent BTK inhibitors, which were optimized from 3z, an EGFR inhibitor previously reported by our group. Among them, compound 24a exhibited great BTK inhibition activity (IC50 = 4.0 nM) and high selectivity in both enzymatic (ITK >250-fold, EGFR >2500-fold) and cellular levels (ITK >227-fold, EGFR 27-fold). In U-937 xenograft models, 24a significantly inhibited tumor growth (TGI = 57.85%) at a 50 mg/kg dosage. Accordingly, 24a is a new BTK inhibitor worthy of further development.
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Affiliation(s)
- Dou Dou
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yanyan Diao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenjie Sha
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Rongrong Su
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Linjiang Tong
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjie Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Limin Leng
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lijuan Xie
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhixiao Yu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Haoming Song
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zihao Shen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hua Xie
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhuo Chen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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6
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Profitós-Pelejà N, Santos JC, Marín-Niebla A, Roué G, Ribeiro ML. Regulation of B-Cell Receptor Signaling and Its Therapeutic Relevance in Aggressive B-Cell Lymphomas. Cancers (Basel) 2022; 14:860. [PMID: 35205606 PMCID: PMC8870007 DOI: 10.3390/cancers14040860] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023] Open
Abstract
The proliferation and survival signals emanating from the B-cell receptor (BCR) constitute a crucial aspect of mature lymphocyte's life. Dysregulated BCR signaling is considered a potent contributor to tumor survival in different subtypes of B-cell non-Hodgkin lymphomas (B-NHLs). In the last decade, the emergence of BCR-associated kinases as rational therapeutic targets has led to the development and approval of several small molecule inhibitors targeting either Bruton's tyrosine kinase (BTK), spleen tyrosine kinase (SYK), or phosphatidylinositol 3 kinase (PI3K), offering alternative treatment options to standard chemoimmunotherapy, and making some of these drugs valuable assets in the anti-lymphoma armamentarium. Despite their initial effectiveness, these precision medicine strategies are limited by primary resistance in aggressive B-cell lymphoma such as diffuse large B-cell lymphoma (DLBCL) and mantle cell lymphoma (MCL), especially in the case of first generation BTK inhibitors. In these patients, BCR-targeting drugs often fail to produce durable responses, and nearly all cases eventually progress with a dismal outcome, due to secondary resistance. This review will discuss our current understanding of the role of antigen-dependent and antigen-independent BCR signaling in DLBCL and MCL and will cover both approved inhibitors and investigational molecules being evaluated in early preclinical studies. We will discuss how the mechanisms of action of these molecules, and their off/on-target effects can influence their effectiveness and lead to toxicity, and how our actual knowledge supports the development of more specific inhibitors and new, rationally based, combination therapies, for the management of MCL and DLBCL patients.
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Affiliation(s)
- Núria Profitós-Pelejà
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; (N.P.-P.); (J.C.S.); (M.L.R.)
| | - Juliana Carvalho Santos
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; (N.P.-P.); (J.C.S.); (M.L.R.)
| | - Ana Marín-Niebla
- Department of Hematology, Experimental Hematology, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Gaël Roué
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; (N.P.-P.); (J.C.S.); (M.L.R.)
| | - Marcelo Lima Ribeiro
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; (N.P.-P.); (J.C.S.); (M.L.R.)
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University Medical School, Braganca Paulista 12916-900, Brazil
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7
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Expanding the armory for treating lymphoma: Targeting redox cellular status through thioredoxin reductase inhibition. Pharmacol Res 2022; 177:106134. [DOI: 10.1016/j.phrs.2022.106134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/12/2022]
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8
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Zimmerman SM, Peer CJ, Figg WD. Ibrutinib's off-target mechanism: cause for dose optimization. Cancer Biol Ther 2021; 22:529-531. [PMID: 34632931 DOI: 10.1080/15384047.2021.1980313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Ibrutinib (Imbruvica®, 2013) is a Bruton's tyrosine kinase (BTK) inhibitor approved for multiple B-cell malignancies and cGVHD. Its treatment is associated with increased risk of cardiac adverse events. Atrial fibrillation is a common cause of therapy discontinuation and interruptions, which have been correlated with shorter progression-free survival in chronic lymphocyte leukemia (CLL) patients. Recently, Xiao et al. identified that ibrutinib-mediated atrial fibrillation is likely due to off-target CSK inhibition. Given promising in vitro and in vivo evidence of maintained biological activity in CLL at lower-than-labeled ibrutinib doses, this elucidated mechanism substantiates the case to investigate alternative dosing schedules. The potential to minimize ibrutinib's off-target effects while conserving response warrants further discussion and investigation of optimal ibrutinib dosing.
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Affiliation(s)
- Sara M Zimmerman
- Clinical Pharmacology Program, Office of the Clinical Director, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cody J Peer
- Clinical Pharmacology Program, Office of the Clinical Director, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - William D Figg
- Clinical Pharmacology Program, Office of the Clinical Director, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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9
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Oliveras JM, Puig de la Bellacasa R, Estrada-Tejedor R, Teixidó J, Borrell JI. 1,6-Naphthyridin-2(1 H)-ones: Synthesis and Biomedical Applications. Pharmaceuticals (Basel) 2021; 14:1029. [PMID: 34681253 PMCID: PMC8539032 DOI: 10.3390/ph14101029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/20/2022] Open
Abstract
Naphthyridines, also known as diazanaphthalenes, are a group of heterocyclic compounds that include six isomeric bicyclic systems containing two pyridine rings. 1,6-Naphthyridines are one of the members of such a family capable of providing ligands for several receptors in the body. Among such structures, 1,6-naphthyridin-2(1H)-ones (7) are a subfamily that includes more than 17,000 compounds (with a single or double bond between C3 and C4) included in more than 1000 references (most of them patents). This review will cover the analysis of the diversity of the substituents present at positions N1, C3, C4, C5, C7, and C8 of 1,6-naphthyridin-2(1H)-ones, the synthetic methods used for their synthesis (both starting from a preformed pyridine or pyridone ring), and the biomedical applications of such compounds.
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Affiliation(s)
| | | | | | | | - José I. Borrell
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain; (J.M.O.); (R.P.d.l.B.); (R.E.-T.); (J.T.)
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10
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Progress in the development of small molecular inhibitors of the Bruton's tyrosine kinase (BTK) as a promising cancer therapy. Bioorg Med Chem 2021; 47:116358. [PMID: 34479103 DOI: 10.1016/j.bmc.2021.116358] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/24/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022]
Abstract
Bruton tyrosine kinase (BTK) is a key kinase in the B cell antigen receptor signal transduction pathway, which is involved in the regulation of the proliferation, differentiation and apoptosis of B cells. BTK has become a significant target for the treatment of hematological malignancies and autoimmune diseases. Ibrutinib, the first-generation BTK inhibitor, has made a great contribution to the treatment of B cell malignant tumors, but there are still some problems such as resistance or miss target of site mutation. Therefore, there is an imperative need to develop novel BTK inhibitors to overcome these problems. Besides, proteolysis targeting chimera (PROTAC) technology has been successfully applied to the development of BTK degradation agents, which has opened a fresh way for the BTK targeted treatment. This paper reviews the biological function of BTK, the discovery and development of BTK targeted drugs as a promising cancer therapy. It mainly reviews the binding sites and structural characteristics of BTK, structure-activity relationships, activity and drug resistance of BTK inhibitors, as well as potential treatment strategies to overcome the resistance of BTK, which provides a reference for the rational design and development of new powerful BTK inhibitors.
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11
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Hu C, Zou F, Wang A, Miao W, Liang Q, Weisberg EL, Wang Y, Liu J, Wang W, Liu Q. Targeting chaperon protein HSP70 as a novel therapeutic strategy for FLT3-ITD-positive acute myeloid leukemia. Signal Transduct Target Ther 2021; 6:334. [PMID: 34521806 PMCID: PMC8440619 DOI: 10.1038/s41392-021-00672-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Fengming Zou
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Aoli Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Weili Miao
- Department of Chemistry, University of California-Riverside, Riverside, CA, USA
| | - Qianmao Liang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California-Riverside, Riverside, CA, USA
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China. .,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China. .,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China. .,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China. .,University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
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12
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Mirzaie S, Abdi F, GhavamiNejad A, Lu B, Wu XY. Covalent Antiviral Agents. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:285-312. [PMID: 34258745 DOI: 10.1007/978-981-16-0267-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Nowadays, many viral infections have emerged and are taking a huge toll on human lives globally. Meanwhile, viral resistance to current drugs has drastically increased. Hence, there is a pressing need to design potent broad-spectrum antiviral agents to treat a variety of viral infections and overcome viral resistance. Covalent inhibitors have the potential to achieve both goals owing to their biochemical efficiency, prolonged duration of action, and the capability to inhibit shallow, solvent-exposed substrate-binding domains. In this chapter, we review the structures, activities, and inhibition mechanisms of covalent inhibitors against severe acute respiratory syndrome coronavirus 2, dengue virus, enterovirus, hepatitis C virus, human immunodeficiency virus, and influenza viruses. We also discuss the application of in silico study in covalent inhibitor design.
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Affiliation(s)
- Sako Mirzaie
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
| | - Fatemeh Abdi
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Amin GhavamiNejad
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Brian Lu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Xiao Yu Wu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
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13
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Tichenor MS, Wiener JJM, Rao NL, Pooley Deckhut C, Barbay JK, Kreutter KD, Bacani GM, Wei J, Chang L, Murrey HE, Wang W, Ahn K, Huber M, Rex E, Coe KJ, Wu J, Seierstad M, Bembenek SD, Leonard KA, Lebsack AD, Venable JD, Edwards JP. Discovery of a Potent and Selective Covalent Inhibitor of Bruton's Tyrosine Kinase with Oral Anti-Inflammatory Activity. ACS Med Chem Lett 2021; 12:782-790. [PMID: 34055226 DOI: 10.1021/acsmedchemlett.1c00044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/28/2021] [Indexed: 11/28/2022] Open
Abstract
Bruton's tyrosine kinase (BTK) is a cytoplasmic tyrosine kinase that plays a critical role in the activation of B cells, macrophages, and osteoclasts. Given the key role of these cell types in the pathology of autoimmune disorders, BTK inhibitors have the potential to improve treatment outcomes in multiple diseases. Herein, we report the discovery and characterization of a novel potent and selective covalent 4-oxo-4,5-dihydro-3H-1-thia-3,5,8-triazaacenaphthylene-2-carboxamide BTK inhibitor chemotype. Compound 27 irreversibly inhibits BTK by targeting a noncatalytic cysteine residue (Cys481) for covalent bond formation. Compound 27 is characterized by selectivity for BTK, potent in vivo BTK occupancy that is sustained after it is cleared from systemic circulation, and dose-dependent efficacy at reducing joint inflammation in a rat collagen-induced arthritis model.
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Affiliation(s)
- Mark S. Tichenor
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - John J. M. Wiener
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Navin L. Rao
- Janssen Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Charlotte Pooley Deckhut
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - J. Kent Barbay
- Janssen Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Kevin D. Kreutter
- Janssen Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Genesis M. Bacani
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Jianmei Wei
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Leon Chang
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Heather E. Murrey
- Janssen Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Weixue Wang
- Janssen Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Kay Ahn
- Janssen Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Michael Huber
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Elizabeth Rex
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Kevin J. Coe
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - JieJun Wu
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Mark Seierstad
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Scott D. Bembenek
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Kristi A. Leonard
- Janssen Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Alec D. Lebsack
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - Jennifer D. Venable
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
| | - James P. Edwards
- Janssen Research & Development, 3210 Merryfield Row, San Diego, California 92121-1126, United States
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14
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Kaur R, Kumar K. Synthetic and medicinal perspective of quinolines as antiviral agents. Eur J Med Chem 2021; 215:113220. [PMID: 33609889 PMCID: PMC7995244 DOI: 10.1016/j.ejmech.2021.113220] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/17/2020] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
Abstract
In current scenario, various heterocycles have come up exhibiting crucial role in various medicinal agents which are valuable for mankind. Out of diverse range of heterocycle, quinoline scaffold have been proved to play an important role in broad range of biological activities. Several drug molecules bearing a quinoline molecule with useful anticancer, antibacterial activities etc have been marketed such as chloroquine, saquinavir etc. Owing to their broad spectrum biological role, various synthetic strategies such as Skraup reaction, Combes reaction etc. has been developed by the researchers all over the world. But still the synthetic methods are associated with various limitations as formation of side products, use of expensive metal catalysts. Thus, several efforts to develop an efficient and cost effective synthetic protocol are still carried out till date. Moreover, quinoline scaffold displays remarkable antiviral activity. Therefore, in this review we have made an attempt to describe recent synthetic protocols developed by various research groups along with giving a complete explanation about the role of quinoline derivatives as antiviral agent. Quinoline derivatives were found potent against various strains of viruses like zika virus, enterovirus, herpes virus, human immunodeficiency virus, ebola virus, hepatitis C virus, SARS virus and MERS virus etc.
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Affiliation(s)
- Ramandeep Kaur
- Department of Pharmaceutical Chemistry, Indo-Soviet Friendship College of Pharmacy (ISFCP), Moga, Punjab, 142001, India
| | - Kapil Kumar
- School of Pharmacy and Technology Management, SVKM's NMIMS, Hyderabad, Telangana, 509301, India.
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15
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Liu J, Chen C, Wang D, Zhang J, Zhang T. Emerging small-molecule inhibitors of the Bruton's tyrosine kinase (BTK): Current development. Eur J Med Chem 2021; 217:113329. [PMID: 33740548 DOI: 10.1016/j.ejmech.2021.113329] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/12/2021] [Accepted: 02/21/2021] [Indexed: 12/29/2022]
Abstract
Therapy based on Bruton's tyrosine kinase (BTK) inhibitors one of the major treatment options currently recommended for lymphoma patients. The first generation of BTK inhibitor, Ibrutinib, achieved remarkable progress in the treatment of B-cell malignancies, but still has problems with drug-resistance or off-target induced serious side effects. Therefore, numerous new BTK inhibitors were developed to address this unmet medical need. In parallel, the effect of BTK inhibitors against immune-related diseases has been evaluated in clinical trials. This review summarizes recent progress in the research and development of BTK inhibitors, with a focus on structural characteristics and structure-activity relationships. The structure-refinement process of representative pharmacophores as well as their effects on binding affinity, biological activity and pharmacokinetics profiles were analyzed. The advantages and disadvantages of reversible/irreversible BTK inhibitors and their potential implications were discussed to provide a reference for the rational design and development of novel potent BTK inhibitors.
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Affiliation(s)
- Jiakuo Liu
- Pharmaceutical Department, PLA Strategic Support Force Medical Center, No.9 Anxiangbeili Road, Chaoyang District, Beijing, 100101, PR China
| | - Chengjuan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China
| | - Dongmei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China
| | - Jie Zhang
- Pharmaceutical Department, PLA Strategic Support Force Medical Center, No.9 Anxiangbeili Road, Chaoyang District, Beijing, 100101, PR China.
| | - Tiantai Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China.
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16
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Yuan S, Zhang J, Zhang D, Wei D, Zuo J, Song J, Yu B, Liu HM. Cu(OTf) 2-Catalyzed Intramolecular Radical Cascade Reactions for the Diversity-Oriented Synthesis of Quinoline-Annulated Polyheterocyclic Frameworks. Org Lett 2021; 23:1445-1450. [PMID: 33560123 DOI: 10.1021/acs.orglett.1c00129] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Compound libraries with high levels of structural diversity and novelty could cover underexploited chemical space and thus have been highly pursued in drug discovery. Herein, we report the first Cu(OTf)2-catalyzed intramolecular radical cascade reactions that enable the diversity-oriented synthesis of quinoline-annulated polyheterocyclic compounds (7 unique scaffolds, 66 examples) in an efficient manner. This work demonstrates an alternative route to access the natural product- and druglike compound collection with high levels of structural diversity and novelty.
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Affiliation(s)
- Shuo Yuan
- School of Pharmaceutical Sciences, Zhengzhou University, Science Road 100, Zhengzhou 450001, China
| | - Jingya Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Science Road 100, Zhengzhou 450001, China
| | - Danqing Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Science Road 100, Zhengzhou 450001, China
| | - Donghui Wei
- College of Chemistry, and Institute of Green Catalysis, Zhengzhou University, Science Road 100, Zhengzhou 450001, China
| | - Jiahui Zuo
- School of Pharmaceutical Sciences, Zhengzhou University, Science Road 100, Zhengzhou 450001, China
| | - Jian Song
- School of Pharmaceutical Sciences, Zhengzhou University, Science Road 100, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Road 100, Zhengzhou 450001, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Road 100, Zhengzhou 450001, China
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17
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Marensi V, Keeshan KR, MacEwan DJ. Pharmacological impact of FLT3 mutations on receptor activity and responsiveness to tyrosine kinase inhibitors. Biochem Pharmacol 2020; 183:114348. [PMID: 33242449 DOI: 10.1016/j.bcp.2020.114348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 01/09/2023]
Abstract
Acute myelogenous leukaemia (AML) is an aggressive blood cancer characterized by the rapid proliferation of immature myeloid blast cells, resulting in a high mortality rate. The 5-year overall survival rate for AML patients is approximately 25%. Circa 35% of all patients carry a mutation in the FLT3 gene which have a poor prognosis. Targeting FLT3 receptor tyrosine kinase has become a treatment strategy in AML patients possessing FLT3 mutations. The most common mutations are internal tandem duplications (ITD) within exon 14 and a single nucleotide polymorphism (SNP) that leads to a point mutation in the D835 of the tyrosine kinase domain (TKD). Variations in the ITD sequence and the occurrence of other point mutations that lead to ligand-independent FLT3 receptor activation create difficulties in developing personalized therapeutic strategies to overcome observed mutation-driven drug resistance. Midostaurin and quizartinib are tyrosine kinase inhibitors (TKIs) with inhibitory efficacy against FLT3-ITD, but exhibit limited clinical impact. In this review, we focus on the structural aspects of the FLT3 receptor and correlate those mutations with receptor activation and the consequences for molecular and clinical responsiveness towards therapies targeting FLT3-ITD positive AML.
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Affiliation(s)
- Vanessa Marensi
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Karen R Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David J MacEwan
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
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18
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Xiao L, Salem JE, Clauss S, Hanley A, Bapat A, Hulsmans M, Iwamoto Y, Wojtkiewicz G, Cetinbas M, Schloss MJ, Tedeschi J, Lebrun-Vignes B, Lundby A, Sadreyev RI, Moslehi J, Nahrendorf M, Ellinor PT, Milan DJ. Ibrutinib-Mediated Atrial Fibrillation Attributable to Inhibition of C-Terminal Src Kinase. Circulation 2020; 142:2443-2455. [PMID: 33092403 DOI: 10.1161/circulationaha.120.049210] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Ibrutinib is a Bruton tyrosine kinase inhibitor with remarkable efficacy against B-cell cancers. Ibrutinib also increases the risk of atrial fibrillation (AF), which remains poorly understood. METHODS We performed electrophysiology studies on mice treated with ibrutinib to assess inducibility of AF. Chemoproteomic analysis of cardiac lysates identified candidate ibrutinib targets, which were further evaluated in genetic mouse models and additional pharmacological experiments. The pharmacovigilance database, VigiBase, was queried to determine whether drug inhibition of an identified candidate kinase was associated with increased reporting of AF. RESULTS We demonstrate that treatment of mice with ibrutinib for 4 weeks results in inducible AF, left atrial enlargement, myocardial fibrosis, and inflammation. This effect was reproduced in mice lacking Bruton tyrosine kinase, but not in mice treated with 4 weeks of acalabrutinib, a more specific Bruton tyrosine kinase inhibitor, demonstrating that AF is an off-target side effect. Chemoproteomic profiling identified a short list of candidate kinases that was narrowed by additional experimentation leaving CSK (C-terminal Src kinase) as the strongest candidate for ibrutinib-induced AF. Cardiac-specific Csk knockout in mice led to increased AF, left atrial enlargement, fibrosis, and inflammation, phenocopying ibrutinib treatment. Disproportionality analyses in VigiBase confirmed increased reporting of AF associated with kinase inhibitors blocking Csk versus non-Csk inhibitors, with a reporting odds ratio of 8.0 (95% CI, 7.3-8.7; P<0.0001). CONCLUSIONS These data identify Csk inhibition as the mechanism through which ibrutinib leads to AF. Registration: URL: https://ww.clinicaltrials.gov; Unique identifier: NCT03530215.
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Affiliation(s)
- Ling Xiao
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Joe-Elie Salem
- Clinical Pharmacology, Sorbonne University, INSERM, APHP, UNICO-GRECO Cardio-oncology Program (J-E.S., B.L-V.), Sorbonne University, ISERM, APHP, UNICO-GRECO Cardio-oncology Program, Hospital Pitié-Salpêtrière, Paris, France.,Clinical Investigation Center, Paris, France (J-E.S.).,Vanderbilt University Medical Center, Cardio-Oncology Program, Division of Cardiovascular Medicine, Nashville, TN (J-E.S., J.M.)
| | - Sebastian Clauss
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Department of Medicine I, Klinikum Grosshadern, University of Munich, Germany (S.C.).,DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Munich Heart Alliance, Germany (S.C.)
| | - Alan Hanley
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Aneesh Bapat
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Maarten Hulsmans
- Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Yoshiko Iwamoto
- Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Gregory Wojtkiewicz
- Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Murat Cetinbas
- Department of Molecular Biology(M.C.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA (M.C.)
| | - Maximilian J Schloss
- Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Justin Tedeschi
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Bénédicte Lebrun-Vignes
- Clinical Pharmacology, Sorbonne University, INSERM, APHP, UNICO-GRECO Cardio-oncology Program (J-E.S., B.L-V.), Sorbonne University, ISERM, APHP, UNICO-GRECO Cardio-oncology Program, Hospital Pitié-Salpêtrière, Paris, France.,Clinical Pharmacology and Regional Pharmacovigilance Center (B.L-V.), Sorbonne University, ISERM, APHP, UNICO-GRECO Cardio-oncology Program, Hospital Pitié-Salpêtrière, Paris, France.,Université Paris Est (UPEC), IRMB- EA 7379 EpiDermE (Epidemiology in Dermatology and Evaluation of Therapeutics), F-94010, Créteil, France (B.L-V.)
| | - Alicia Lundby
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences and NNF Center for Protein Research, Københavns Universitet, Copenhagen, Denmark (A.L.)
| | - Ruslan I Sadreyev
- Department of Pathology (R.I.S.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Javid Moslehi
- Vanderbilt University Medical Center, Cardio-Oncology Program, Division of Cardiovascular Medicine, Nashville, TN (J-E.S., J.M.)
| | - Matthias Nahrendorf
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Patrick T Ellinor
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E.)
| | - David J Milan
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Leducq Foundation, Boston, MA (D.J.M.)
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19
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Hanan EJ, Liang J, Wang X, Blake RA, Blaquiere N, Staben ST. Monomeric Targeted Protein Degraders. J Med Chem 2020; 63:11330-11361. [DOI: 10.1021/acs.jmedchem.0c00093] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Jeong S, Sohn YK, Choi Y, Park J, Kim HS. A regulatory SH2 domain-targeting protein binder effectively inhibits the activity of Bruton's tyrosine kinase and its drug-resistant variants. Biochem Biophys Res Commun 2020; 526:8-13. [PMID: 32192770 DOI: 10.1016/j.bbrc.2020.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 01/06/2023]
Abstract
Human Bruton's tyrosine kinase (hBtk) plays a key role in growth and metabolism of B cells, but its dysfunctions cause various B-cell malignancies. Inhibitors targeting the ATP-binding pocket of hBtk have been developed, but they have several drawbacks such as adverse side effects and occurrence of drug-resistant mutations. Here, we present a protein binder which specifically binds to an allosteric regulatory SH2 domain of hBtk. The protein binder effectively inhibited the hBtk activity, indicating a critical role of the SH2 domain in allosteric regulation of the hBtk activity. Cytosolic delivery of the protein binder led to a significant inhibition on the BCR-mediated signaling and viability of B lymphoma cells. The utility of our approach was demonstrated by effective inhibition of drug-resistant hBtk variants by the protein binder. Based on the computationally predicted binding mode, the protein binder is likely to inhibit the hBtk activity by disrupting the interaction between the SH2 domain and kinase domain. The present approach can be used for developing therapeutic agents with improved efficacy for B-cell lymphoma.
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Affiliation(s)
- Sukyo Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Yoo-Kyoung Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Yoonjoo Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Jinho Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
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21
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de Wispelaere M, Carocci M, Burri DJ, Neidermyer WJ, Olson CM, Roggenbach I, Liang Y, Wang J, Whelan SPJ, Gray NS, Yang PL. A broad-spectrum antiviral molecule, QL47, selectively inhibits eukaryotic translation. J Biol Chem 2020; 295:1694-1703. [PMID: 31914414 PMCID: PMC7008383 DOI: 10.1074/jbc.ra119.011132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
Small-molecule inhibitors of translation are critical tools to study the molecular mechanisms of protein synthesis. In this study, we sought to characterize how QL47, a host-targeted, small-molecule antiviral agent, inhibits steady-state viral protein expression. We demonstrate that this small molecule broadly inhibits both viral and host protein synthesis and targets a translation step specific to eukaryotic cells. We show that QL47 inhibits protein neosynthesis initiated by both canonical cap-driven and noncanonical initiation strategies, most likely by targeting an early step in translation elongation. Our findings thus establish QL47 as a new small-molecule inhibitor that can be utilized to probe the eukaryotic translation machinery and that can be further developed as a new therapeutic agent.
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Affiliation(s)
- Mélissanne de Wispelaere
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Margot Carocci
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Dominique J Burri
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - William J Neidermyer
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Calla M Olson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Imme Roggenbach
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Yanke Liang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Sean P J Whelan
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Priscilla L Yang
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115.
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22
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Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
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Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
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23
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Gui F, Jiang J, He Z, Li L, Li Y, Deng Z, Lu Y, Wu X, Chen G, Su J, Song S, Zhang Y, Yun C, Huang X, Weisberg E, Zhang J, Deng X. A non-covalent inhibitor XMU-MP-3 overrides ibrutinib-resistant Btk C481S mutation in B-cell malignancies. Br J Pharmacol 2019; 176:4491-4509. [PMID: 31364164 PMCID: PMC6932946 DOI: 10.1111/bph.14809] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 07/06/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND PURPOSE Bruton's tyrosine kinase (BTK) plays a key role in B-cell receptor signalling by regulating cell proliferation and survival in various B-cell malignancies. Covalent low-MW BTK kinase inhibitors have shown impressive clinical efficacy in B-cell malignancies. However, the mutant BtkC481S poses a major challenge in the management of B-cell malignancies by disrupting the formation of the covalent bond between BTK and irreversible inhibitors, such as ibrutinib. The present studies were designed to develop novel BTK inhibitors targeting ibrutinib-resistant BtkC481S mutation. EXPERIMENTAL APPROACH BTK-Ba/F3, BTK(C481S)-Ba/F3 cells, and human malignant B-cells JeKo-1, Ramos, and NALM-6 were used to evaluate cellular potency of BTK inhibitors. The in vitro pharmacological efficacy and compound selectivity were assayed via cell viability, colony formation, and BTK-mediated signalling. A tumour xenograft model with BTK-Ba/F3, Ramos and BTK(C481S)-Ba/F3 cells in Nu/nu BALB/c mice was used to assess in vivo efficacy of XMU-MP-3. KEY RESULTS XMU-MP-3 is one of a group of low MW compounds that are potent non-covalent BTK inhibitors. XMU-MP-3 inhibited both BTK and the acquired mutant BTKC481S, in vitro and in vivo. Further computational modelling, site-directed mutagenesis analysis, and structure-activity relationships studies indicated that XMU-MP-3 displayed a typical Type-II inhibitor binding mode. CONCLUSION AND IMPLICATIONS XMU-MP-3 directly targets the BTK signalling pathway in B-cell lymphoma. These findings establish XMU-MP-3 as a novel inhibitor of BTK, which could serve as both a tool compound and a lead for further drug development in BTK relevant B-cell malignancies, especially those with the acquired ibrutinib-resistant C481S mutation.
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MESH Headings
- Adenine/analogs & derivatives
- Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors
- Agammaglobulinaemia Tyrosine Kinase/genetics
- Agammaglobulinaemia Tyrosine Kinase/metabolism
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Cells, Cultured
- Dose-Response Relationship, Drug
- Drug Resistance, Neoplasm/drug effects
- Drug Screening Assays, Antitumor
- Female
- HEK293 Cells
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Molecular Docking Simulation
- Molecular Structure
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Piperidines
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Pyrazoles/chemistry
- Pyrazoles/pharmacology
- Pyrimidines/chemistry
- Pyrimidines/pharmacology
- Signal Transduction/drug effects
- Structure-Activity Relationship
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Affiliation(s)
- Fu Gui
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Jie Jiang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Zhixiang He
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Li Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Yunzhan Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Zhou Deng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Yue Lu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Xinrui Wu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Guyue Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Jingyi Su
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Siyang Song
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
| | - Yue‐Ming Zhang
- Institute of Systems Biomedicine, Department of Biophysics and Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Cai‐Hong Yun
- Institute of Systems Biomedicine, Department of Biophysics and Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Xin Huang
- Division of Drug Discovery, Hongyun Biotech Co., Ltd.NanjingChina
| | - Ellen Weisberg
- Department of Medical Oncology, Dana Farber Cancer InstituteHarvard Medical SchoolBostonMassachusetts
| | - Jianming Zhang
- National Research Center for Translational Medicine, Shanghai State Key Laboratory of Medical Genomics, Rui‐Jin HospitalShanghai JiaoTong University School of MedicineShanghaiChina
- Cutaneous Biology Research Center, Massachusetts General HospitalHarvard Medical SchoolBostonMassachusetts
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State‐Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life ScienceXiamen UniversityXiamenChina
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Guo X, Yang D, Fan Z, Zhang N, Zhao B, Huang C, Wang F, Ma R, Meng M, Deng Y. Discovery and structure-activity relationship of novel diphenylthiazole derivatives as BTK inhibitor with potent activity against B cell lymphoma cell lines. Eur J Med Chem 2019; 178:767-781. [DOI: 10.1016/j.ejmech.2019.06.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/09/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
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25
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Sharma A, Thelma BK. Pharmacophore modeling and virtual screening in search of novel Bruton's tyrosine kinase inhibitors. J Mol Model 2019; 25:179. [PMID: 31172362 DOI: 10.1007/s00894-019-4047-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/23/2019] [Indexed: 12/11/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a known drug target for B cell malignancies and autoimmune diseases like rheumatoid arthritis. Consequently, efforts to develop BTK inhibitors have gained momentum in the last decade, resulting in a number of potential inhibitory molecules. However, to date, there are only two FDA approved drugs for B cell malignancies (Ibrutinib and Acalabrutinib), thus continued efforts are warranted. A large number of molecular scaffolds with potential BTK inhibitory activity are already available from these studies, and therefore we employed a ligand-based approach towards computer-aided drug design to develop a pharmacophore model for BTK inhibitors. Using over 400 molecules with known half maximal inhibitory concentrations (IC50) for BTK, a four-point pharmacophore hypothesis was derived, with two aromatic rings (R), one hydrogen bond acceptor (A) and one hydrogen bond donor (D). Screening of two small-molecule databases against this pharmacophore returned 620 hits with matching chemical features. Docking these against the ATP-binding site of the BTK kinase domain through a virtual screening workflow yielded 30 hits from which ultimately two natural compounds (two best scoring poses for each) were prioritized. Molecular dynamics simulations of these four docked complexes confirmed the stability of protein-ligand binding over a 200 ns time period, and thus their suitability for lead molecule development with further optimization and experimental testing. Of note, the pharmacophore model developed in this study would also be further useful for de novo drug design and virtual screening efforts on a larger scale. Graphical abstract Pharmacophore modeling and virtual screening in search of novel Bruton's tyrosine kinase inhibitors.
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Affiliation(s)
- Aditya Sharma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India.
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26
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Liu L, Li X, Cheng Y, Wang L, Yang H, Li J, He S, shuangjie Wu, Yin Q, Xiang H. Optimization of novel benzofuro[3,2-b]pyridin-2(1H)-one derivatives as dual inhibitors of BTK and PI3Kδ. Eur J Med Chem 2019; 164:304-316. [DOI: 10.1016/j.ejmech.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/08/2018] [Accepted: 12/22/2018] [Indexed: 11/30/2022]
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27
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Castro-Falcón G, Seiler GS, Demir Ö, Rathinaswamy MK, Hamelin D, Hoffmann RM, Makowski SL, Letzel AC, Field SJ, Burke JE, Amaro RE, Hughes CC. Neolymphostin A Is a Covalent Phosphoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor That Employs an Unusual Electrophilic Vinylogous Ester. J Med Chem 2018; 61:10463-10472. [PMID: 30380865 PMCID: PMC6688905 DOI: 10.1021/acs.jmedchem.8b00975] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using a novel chemistry-based assay for identifying electrophilic natural products in unprocessed extracts, we identified the PI3-kinase/mTOR dual inhibitor neolymphostin A from Salinispora arenicola CNY-486. The method further showed that the vinylogous ester substituent on the neolymphostin core was the exact site for enzyme conjugation. Tandem MS/MS experiments on PI3Kα treated with the inhibitor revealed that neolymphostin covalently modified Lys802 with a shift in mass of +306 amu, corresponding to addition of the inhibitor and elimination of methanol. The binding pose of the inhibitor bound to PI3Kα was modeled, and hydrogen-deuterium exchange mass spectrometry experiments supported this model. Against a panel of kinases, neolymphostin showed good selectivity for PI3-kinase and mTOR. In addition, the natural product blocked AKT phosphorylation in live cells with an IC50 of ∼3 nM. Taken together, neolymphostin is the first reported example of a covalent kinase inhibitor from the bacterial domain of life.
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Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA, 92093
- These authors contributed equally to this work
| | - Grant S. Seiler
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA, 92093
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA, 92093
- These authors contributed equally to this work
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA, 92093
| | - Manoj K. Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
| | - David Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
| | - Reece M. Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
| | - Stefanie L. Makowski
- School of Medicine, University of California, San Diego, La Jolla, California, USA, 92093
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA, 92093
| | - Seth J. Field
- School of Medicine, University of California, San Diego, La Jolla, California, USA, 92093
| | - John E. Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA, 92093
| | - Chambers C. Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA, 92093
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28
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Amaral PDA, Autheman D, de Melo GD, Gouault N, Cupif JF, Goyard S, Dutra P, Coatnoan N, Cosson A, Monet D, Saul F, Haouz A, Uriac P, Blondel A, Minoprio P. Designed mono- and di-covalent inhibitors trap modeled functional motions for Trypanosoma cruzi proline racemase in crystallography. PLoS Negl Trop Dis 2018; 12:e0006853. [PMID: 30372428 PMCID: PMC6224121 DOI: 10.1371/journal.pntd.0006853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/08/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
Chagas disease, caused by Trypanosoma cruzi, affects millions of people in South America and no satisfactory therapy exists, especially for its life threatening chronic phase. We targeted the Proline Racemase of T. cruzi, which is present in all stages of the parasite life cycle, to discover new inhibitors against this disease. The first published crystal structures of the enzyme revealed that the catalytic site is too small to allow any relevant drug design. In previous work, to break through the chemical space afforded to virtual screening and drug design, we generated intermediate models between the open (ligand free) and closed (ligand bound) forms of the enzyme. In the present work, we co-crystallized the enzyme with the selected inhibitors and found that they were covalently bound to the catalytic cysteine residues in the active site, thus explaining why these compounds act as irreversible inhibitors. These results led us to the design of a novel, more potent specific inhibitor, NG-P27. Co-crystallization of this new inhibitor with the enzyme allowed us to confirm the predicted protein functional motions and further characterize the chemical mechanism. Hence, the catalytic Cys300 sulfur atom of the enzyme attacks the C2 carbon of the inhibitor in a coupled, regiospecific—stereospecific Michael reaction with trans-addition of a proton on the C3 carbon. Strikingly, the six different conformations of the catalytic site in the crystal structures reported in this work had key similarities to our intermediate models previously generated by inference of the protein functional motions. These crystal structures span a conformational interval covering roughly the first quarter of the opening mechanism, demonstrating the relevance of modeling approaches to break through chemical space in drug design. There is an urgent need to develop innovative medicines addressing neglected diseases, multi-drug resistance and other unmet therapeutic needs. To create new drug design opportunities, we attempted to exploit protein functional motions by using a rational approach to model structural intermediates of a therapeutic target. After successfully designing inhibitors based on modeled intermediates of T. Cruzi proline racemase, the determination of crystal structures of the target protein in complex with the inhibitors revealed conformations that were strikingly close to the predicted models. Thus, beyond the discovery of compounds establishing a novel mode of action that can lead to innovative treatments of Chagas disease, we illustrate how modeling protein functional motions can be exploited in a rational approach to create opportunities in drug design.
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Affiliation(s)
- Patricia de Aguiar Amaral
- Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France
| | - Delphine Autheman
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Guilherme Dias de Melo
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Nicolas Gouault
- Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France
| | - Jean-François Cupif
- Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France
| | - Sophie Goyard
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Patricia Dutra
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Nicolas Coatnoan
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Alain Cosson
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Damien Monet
- Institut Pasteur, Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France
| | - Frederick Saul
- Institut Pasteur, Plateforme de Cristallographie, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Plateforme de Cristallographie, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France
| | - Philippe Uriac
- Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France
- * E-mail: (PU); (AB); (PM)
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France
- * E-mail: (PU); (AB); (PM)
| | - Paola Minoprio
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
- * E-mail: (PU); (AB); (PM)
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29
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Lu S, Zhao K, Wang X, Liu H, Ainiwaer X, Xu Y, Ye M. Use of Laplacian Heat Diffusion Algorithm to Infer Novel Genes With Functions Related to Uveitis. Front Genet 2018; 9:425. [PMID: 30349554 PMCID: PMC6186792 DOI: 10.3389/fgene.2018.00425] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022] Open
Abstract
Uveitis is the inflammation of the uvea and is a serious eye disease that can cause blindness for middle-aged and young people. However, the pathogenesis of this disease has not been fully uncovered and thus renders difficulties in designing effective treatments. Completely identifying the genes related to this disease can help improve and accelerate the comprehension of uveitis. In this study, a new computational method was developed to infer potential related genes based on validated ones. We employed a large protein–protein interaction network reported in STRING, in which Laplacian heat diffusion algorithm was applied using validated genes as seed nodes. Except for the validated ones, all genes in the network were filtered by three tests, namely, permutation, association, and function tests, which evaluated the genes based on their specialties and associations to uveitis. Results indicated that 59 inferred genes were accessed, several of which were confirmed to be highly related to uveitis by literature review. In addition, the inferred genes were compared with those reported in a previous study, indicating that our reported genes are necessary supplements.
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Affiliation(s)
- Shiheng Lu
- Department of Ophthalmology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, China
| | - Ke Zhao
- Department of Ophthalmology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, China
| | - Xuefei Wang
- Department of Ophthalmology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, China
| | - Hui Liu
- Department of Ophthalmology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, China
| | - Xiamuxiya Ainiwaer
- Department of Ophthalmology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, China
| | - Yan Xu
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Min Ye
- Department of Ophthalmology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, China
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30
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Elsayed MSA, Griggs B, Cushman M. Synthesis of Benzo[1,6]naphthyridinones Using the Catellani Reaction. Org Lett 2018; 20:5228-5232. [DOI: 10.1021/acs.orglett.8b02171] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mohamed S. A. Elsayed
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brittany Griggs
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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31
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Liu L, Shi B, Li X, Wang X, Lu X, Cai X, Huang A, Luo G, You Q, Xiang H. Design and synthesis of benzofuro[3,2-b]pyridin-2(1H)-one derivatives as anti-leukemia agents by inhibiting Btk and PI3Kδ. Bioorg Med Chem 2018; 26:4537-4543. [DOI: 10.1016/j.bmc.2018.07.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/18/2018] [Accepted: 07/26/2018] [Indexed: 12/17/2022]
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32
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Wang C, Li S, Meng Q, Sun X, Li H, Shu X, Sun H, Liu K, Liu Z, Ma X. Novel amino acid-substituted diphenylpyrimidine derivatives as potent BTK inhibitors against B cell lymphoma cell lines. Bioorg Med Chem 2018; 26:4179-4186. [DOI: 10.1016/j.bmc.2018.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
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33
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Zhang Z, Zhang D, Liu Y, Yang D, Ran F, Wang ML, Zhao G. Targeting Bruton's tyrosine kinase for the treatment of B cell associated malignancies and autoimmune diseases: Preclinical and clinical developments of small molecule inhibitors. Arch Pharm (Weinheim) 2018; 351:e1700369. [DOI: 10.1002/ardp.201700369] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Zhen Zhang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Daoguang Zhang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Yang Liu
- The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Dezhi Yang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Fansheng Ran
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Michael L. Wang
- The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Guisen Zhao
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
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34
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Yu CH, Chou CC, Tu HF, Huang WC, Ho YY, Khoo KH, Lee MS, Chang GD. Antibody-assisted target identification reveals afatinib, an EGFR covalent inhibitor, down-regulating ribonucleotide reductase. Oncotarget 2018; 9:21512-21529. [PMID: 29765556 PMCID: PMC5940374 DOI: 10.18632/oncotarget.25177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 04/05/2018] [Indexed: 01/14/2023] Open
Abstract
Afatinib, used for the first-line treatment of non-small-cell lung carcinoma (NSCLC) patients with distinct epidermal growth factor receptor (EGFR) mutations, inactivates EGFR by mimicking ATP structure and forming a covalent adduct with EGFR. We developed a method to unravel potential targets of afatinib in NSCLC cells through immunoprecipitation of afatinib-labeling proteins with anti-afatinib antiserum and mass spectrometry analysis. Ribonucleotide reductase (RNR) is one of target proteins of afatinib revealed by this method. Treatment of afatinib at 10-100 nM potently inhibited intracellular RNR activity in an in vitro assay using permeabilized PC-9 cells (formerly known as PC-14). PC-9 cells treated with 10 μM afatinib displayed elevated markers of DNA damage. Long-term treatment of therapeutic concentrations of afatinib in PC-9 cells caused significant decrease in protein levels of RNR subunit M2 at 1-10 nM and RNR subunit M1 at 100 nM. EGFR-null Chinese hamster ovary (CHO) cells treated with afatinib also showed similar effects. Afatinib repressed the upregulation of RNR subunit M2 induced by gemcitabine. Covalent modification with afatinib resulting in inhibition and protein downregulation of RNR underscores the therapeutic and off-target effects of afatinib. Afatinib may serve as a lead compound of chemotherapeutic drugs targeting RNR. This method can be widely used in the identification of potential targets of other covalent drugs.
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Affiliation(s)
- Cheng-Han Yu
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Fang Tu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Wei-Chieh Huang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Ya-Yeh Ho
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Kay-Hooi Khoo
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Shyue Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Geen-Dong Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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35
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Rauf F, Festa F, Park JG, Magee M, Eaton S, Rinaldi C, Betanzos CM, Gonzalez-Malerva L, LaBaer J. Ibrutinib inhibition of ERBB4 reduces cell growth in a WNT5A-dependent manner. Oncogene 2018; 37:2237-2250. [PMID: 29398709 PMCID: PMC5916919 DOI: 10.1038/s41388-017-0079-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/25/2017] [Accepted: 11/03/2017] [Indexed: 12/25/2022]
Abstract
Alterations in ERBB family members have been associated with many tumor malignancies. EGFR and ERBB2 have been extensively explored in clinical oncology and several drugs currently target them therapeutically. However, the significance of ERBB4 as a potential therapeutic target remains mostly unexplored, even though ERBB4 is overexpressed or mutated in many solid tumors. Using a unique functional protein microarray platform, we found that ibrutinib inhibits ERBB4 activity in the same nM range as its canonical target, BTK. Cell-based assays revealed that ibrutinib treatment inhibited cell growth and decreased phosphorylation of ERBB4 and downstream targets MEK and ERK in cancer cell lines with high levels of endogenous ERBB4. In vivo, ibrutinib-responsive mouse xenograft tumors showed decreased tumor volumes with ibrutinib treatment. Interestingly, global gene expression comparisons between responsive and non-responsive cells identified a signature featuring the WNT pathway that predicts growth responsiveness to ibrutinib. Non-responsive ERBB4-expressing cell lines featured elevated activity of the WNT pathway, through the overexpression of WNT5A. Moreover, inhibition of WNT5A expression led to an ibrutinib response in non-responsive cell lines. Our data show that inhibiting ERBB4 reduces cell growth in cells that have low WNT5A expression and reveal a link between the ERBB4 and WNT pathways.
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Affiliation(s)
- Femina Rauf
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Fernanda Festa
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jin G Park
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Mitchell Magee
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Seron Eaton
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Capria Rinaldi
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Carlos Morales Betanzos
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Laura Gonzalez-Malerva
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joshua LaBaer
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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36
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Jones LH. Small-Molecule Kinase Downregulators. Cell Chem Biol 2018; 25:30-35. [DOI: 10.1016/j.chembiol.2017.10.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/01/2017] [Accepted: 10/24/2017] [Indexed: 12/28/2022]
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37
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Li H, Sun W, Huang X, Lu X, Patel PR, Kim M, Orr MJ, Fisher RM, Tanaka TQ, McKew JC, Simeonov A, Sanderson PE, Zheng W, Williamson KC, Huang W. Efficient Synthesis of 1,9-Substituted Benzo[h][1,6]naphthyridin-2(1H)-ones and Evaluation of their Plasmodium falciparum Gametocytocidal Activities. ACS COMBINATORIAL SCIENCE 2017; 19:748-754. [PMID: 29024590 DOI: 10.1021/acscombsci.7b00119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel three-component, two-step, one-pot nucleophilic aromatic substitution (SNAr)-intramolecular cyclization-Suzuki coupling reaction was developed for the synthesis of benzo[h][1,6]naphthyridin-2(1H)-ones (Torins). On the basis of the new efficiently convergent synthetic route, a library of Torin analogs was synthesized. The antimalarial activities of these compounds were evaluated against asexual parasites using a growth inhibition assay and gametocytes using a viability assay.
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Affiliation(s)
- Hao Li
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wei Sun
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Xiuli Huang
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Xiao Lu
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Paresma R. Patel
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Myunghoon Kim
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Meghan J. Orr
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard M. Fisher
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Takeshi Q Tanaka
- Laboratory
of Malaria and Vector Research, National Institute of Allergy and
Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - John C. McKew
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Philip E. Sanderson
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wei Zheng
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kim C. Williamson
- Department
of Biology, Loyola University Chicago, Chicago, Illinois 60660, United States
- Microbiology
and Immunology Department, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814, United States
| | - Wenwei Huang
- National
Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
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38
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Wang L, Zhao J, Yao Y, Wang C, Zhang J, Shu X, Sun X, Li Y, Liu K, Yuan H, Ma X. Covalent binding design strategy: A prospective method for discovery of potent targeted anticancer agents. Eur J Med Chem 2017; 142:493-505. [DOI: 10.1016/j.ejmech.2017.09.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/16/2022]
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39
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Ge Y, Wang C, Song S, Huang J, Liu Z, Li Y, Meng Q, Zhang J, Yao J, Liu K, Ma X, Sun X. Identification of highly potent BTK and JAK3 dual inhibitors with improved activity for the treatment of B-cell lymphoma. Eur J Med Chem 2017; 143:1847-1857. [PMID: 29146136 DOI: 10.1016/j.ejmech.2017.10.080] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/24/2017] [Accepted: 10/30/2017] [Indexed: 01/05/2023]
Abstract
The BTK and JAK3 receptor tyrosine kinases are two validated and therapeutically amenable targets in the treatment of B-cell lymphomas. Here we report the identification of several classes of pyrimidine derivatives as potent BTK and JAK3 dual inhibitors. Among these molecules, approximately two thirds displayed strong inhibitory capacity at less than 10 nM concentration, and four compounds (7e, 7g, 7m and 7n) could significantly inhibit the phosphorylation of BTK and JAK3 enzymes at concentrations lower than 1 nM. Additionally, these pyrimidine derivatives also exhibited enhanced activity to block the proliferation of B-cell lymphoma cells compared with the representative BTK inhibitor ibrutinib. In particular, two structure-specific compounds 7b and 7e displayed stronger activity than reference agents in cell-based evaluation, with IC50 values lower than 10 μM. Further biological studies, including flow cytometric analysis, and a xenograft model for in vivo evaluation, also indicated their efficacy and low toxicity in the treatment of B-cell lymphoma. These findings provide a new insight for the development of novel anti-B-cell lymphoma drugs with multi-target actions.
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Affiliation(s)
- Yang Ge
- Department of Hematology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, PR China; College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Changyuan Wang
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Shijie Song
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Jiaxin Huang
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Zhihao Liu
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Yongming Li
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Qiang Meng
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Jianbin Zhang
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Jihong Yao
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Kexin Liu
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China
| | - Xiaodong Ma
- College of Pharmacy, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, PR China.
| | - Xiuli Sun
- Department of Hematology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, PR China.
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40
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Dittus L, Werner T, Muelbaier M, Bantscheff M. Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors. ACS Chem Biol 2017; 12:2515-2521. [PMID: 28876896 DOI: 10.1021/acschembio.7b00617] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemoproteomics profiling of kinase inhibitors with kinobeads enables the assessment of inhibitor potency and selectivity for endogenously expressed protein kinases in cell lines and tissues. Using a small panel of targeted covalent inhibitors, we demonstrate the importance of measuring covalent target binding in live cells. We present a differential kinobeads profiling strategy for covalent kinase inhibitors where a compound is added either to live cells or to a cell extract that enables the comprehensive assessment of inhibitor selectivity for covalent and noncovalent targets. We found that Acalabrutinib, CC-292, and Ibrutinib potently and covalently bind TEC family kinases, but only Ibrutinib also potently binds to BLK. ZAK was identified as a submicromolar affinity Ibrutinib off-target due to covalent modification of Cys22. In contrast to Ibrutinib, 5Z-7-Oxozeaenol reacted with Cys150 next to the DFG loop, demonstrating an alternative route to covalent inactivation of this kinase, e.g., to inhibit canonical TGF-β dependent processes.
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Affiliation(s)
- Lars Dittus
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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41
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Structure-activity relationship investigation for benzonaphthyridinone derivatives as novel potent Bruton's tyrosine kinase (BTK) irreversible inhibitors. Eur J Med Chem 2017. [PMID: 28628824 DOI: 10.1016/j.ejmech.2017.06.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Through a structure-based drug design approach, a tricyclic benzonaphthyridinone pharmacophore was used as a starting point for carrying out detailed medicinal structure-activity relationhip (SAR) studies geared toward characterization of a panel of proposed BTK inhibitors, including 6 (QL-X-138), 7 (BMX-IN-1) and 8 (QL47). These studies led to the discovery of the novel potent irreversible BTK inhibitor, compound 18 (CHMFL-BTK-11). Kinetic analysis of compound 18 revealed an irreversible binding efficacy (kinact/Ki) of 0.01 μM-1s-1. Compound 18 potently inhibited BTK kinase Y223 auto-phosphorylation (EC50 < 100 nM), arrested cell cycle in G0/G1 phase, and induced apoptosis in Ramos, MOLM13 and Pfeiffer cells. We believe these features would make 18 a good pharmacological tool for studying BTK-related pathologies.
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42
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Field SD, Arkin J, Li J, Jones LH. Selective Downregulation of JAK2 and JAK3 by an ATP-Competitive pan-JAK Inhibitor. ACS Chem Biol 2017; 12:1183-1187. [PMID: 28318222 DOI: 10.1021/acschembio.7b00116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PF-956980 has been used previously as a JAK3-selective chemical probe in numerous cell-based experiments. Here, we report that not only is PF-956980 a pan-JAK ATP-competitive inhibitor but it also causes selective reduction of endogenous JAK2 and JAK3 protein levels in human primary immune cells (in a time-dependent manner), leaving the other JAK family members (JAK1 and TYK2) unchanged. We found that PF-956980 selectively downregulated JAK2 and JAK3 mRNA, corresponding to changes observed at the protein level. This work highlights therapeutic opportunities for the development of pharmacological inhibitors that also modulate the expression of their cognate binding proteins.
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Affiliation(s)
- S. Denise Field
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jacob Arkin
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jing Li
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Lyn H. Jones
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
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43
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Liu H, Qu M, Xu L, Han X, Wang C, Shu X, Yao J, Liu K, Peng J, Li Y, Ma X. Design and synthesis of sulfonamide-substituted diphenylpyrimidines (SFA-DPPYs) as potent Bruton's tyrosine kinase (BTK) inhibitors with improved activity toward B-cell lymphoblastic leukemia. Eur J Med Chem 2017; 135:60-69. [PMID: 28432946 DOI: 10.1016/j.ejmech.2017.04.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/31/2022]
Abstract
A new series of diphenylpyrimidine derivatives (SFA-DPPYs) were synthesized by introducing a functional sulfonamide into the C-2 aniline moiety of pyrimidine template, and then were biologically evaluated as potent Bruton's tyrosine kinase (BTK) inhibitors. Among these molecules, inhibitors 10c, 10i, 10j and 10k displayed high potency against the BTK enzyme, with IC50 values of 1.18 nM, 0.92 nM, 0.42 nM and 1.05 nM, respectively. In particular, compound 10c could remarkably inhibit the proliferation of the B lymphoma cell lines at concentrations of 6.49 μM (Ramos cells) and 13.2 μM (Raji cells), and was stronger than the novel agent spebrutinib. In addition, the inhibitory potency toward the normal PBMC cells showed that inhibitor 10c possesses low cell cytotoxicity. All these explorations indicated that molecule 10c could serve as a valuable inhibitor for B-cell lymphoblastic leukemia treatment.
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Affiliation(s)
- He Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Menghua Qu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Lina Xu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Xu Han
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Changyuan Wang
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Xiaohong Shu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Jihong Yao
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Kexin Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Jinyong Peng
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Yanxia Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, PR China
| | - Xiaodong Ma
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China.
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44
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Liang Y, de Wispelaere M, Carocci M, Liu Q, Wang J, Yang PL, Gray NS. Structure-Activity Relationship Study of QL47: A Broad-Spectrum Antiviral Agent. ACS Med Chem Lett 2017; 8:344-349. [PMID: 28337328 PMCID: PMC5346993 DOI: 10.1021/acsmedchemlett.7b00008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/03/2017] [Indexed: 11/30/2022] Open
Abstract
Here we report the structure-activity relationship (SAR) investigations of QL-XII-47 (QL47), a compound that possesses broad-spectrum antiviral activity against dengue virus and other RNA viruses. A medicinal chemistry campaign initiated from QL47, a previously reported covalent BTK inhibitor, to derive YKL-04-085, which is devoid of any kinase activity when screened against a panel of 468 kinases and with improved pharmacokinetic properties. Both QL47 and YKL-04-085 are potent inhibitors of viral translation and exhibit cellular antiviral activity at 35-fold lower concentrations relative to inhibition of host-cell proliferation.
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Affiliation(s)
- Yanke Liang
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Departments of Biological Chemistry & Molecular
Pharmacology and Microbiology and
Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Melissanne de Wispelaere
- Departments of Biological Chemistry & Molecular
Pharmacology and Microbiology and
Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Margot Carocci
- Departments of Biological Chemistry & Molecular
Pharmacology and Microbiology and
Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qingsong Liu
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Departments of Biological Chemistry & Molecular
Pharmacology and Microbiology and
Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jinhua Wang
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Departments of Biological Chemistry & Molecular
Pharmacology and Microbiology and
Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Priscilla L. Yang
- Departments of Biological Chemistry & Molecular
Pharmacology and Microbiology and
Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nathanael S. Gray
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Departments of Biological Chemistry & Molecular
Pharmacology and Microbiology and
Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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45
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Liang Q, Chen Y, Yu K, Chen C, Zhang S, Wang A, Wang W, Wu H, Liu X, Wang B, Wang L, Hu Z, Wang W, Ren T, Zhang S, Liu Q, Yun CH, Liu J. Discovery of N-(3-(5-((3-acrylamido-4-(morpholine-4-carbonyl)phenyl)amino)-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-2-methylphenyl)-4-(tert-butyl)benzamide (CHMFL-BTK-01) as a highly selective irreversible Bruton's tyrosine kinase (BTK) inhibitor. Eur J Med Chem 2017; 131:107-125. [PMID: 28315597 DOI: 10.1016/j.ejmech.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 10/20/2022]
Abstract
Currently there are several irreversible BTK inhibitors targeting Cys481 residue under preclinical or clinical development. However, most of these inhibitors also targeted other kinases such as BMX, JAK3, and EGFR that bear the highly similar active cysteine residues. Through a structure-based drug design approach, we discovered a highly potent (IC50: 7 nM) irreversible BTK inhibitor compound 9 (CHMFL-BTK-01), which displayed a high selectivity profile in KINOMEscan (S score (35) = 0.00) among 468 kinases/mutants at the concentration of 1 μM. Compound 9 completely abolished BMX, JAK3 and EGFR's activity. Both X-ray crystal structure and cysteine-serine mutation mediated rescue experiment confirmed 9's irreversible binding mode. 9 also potently inhibited BTK Y223 auto-phosphorylation (EC50: <30 nM), arrested cell cycle in G0/G1 phase and induced apoptosis in U2932 and Pfeiffer cells. We believe these features would make 9 a good pharmacological tool to study the BTK related pathology.
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Affiliation(s)
- Qianmao Liang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230036, PR China; High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Yongfei Chen
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Kailin Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230036, PR China
| | - Cheng Chen
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Shouxiang Zhang
- Institute of Systems Biomedicine, Department of Biophysics, Beijing Key Laboratory of Tumor Systems Biology and Center for Molecular and Translational Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, PR China
| | - Aoli Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230036, PR China
| | - Wei Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Hong Wu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230036, PR China
| | - Xiaochuan Liu
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230036, PR China; High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Beilei Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Li Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Zhenquan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Wenchao Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Tao Ren
- Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230088, PR China
| | - Shanchun Zhang
- CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; Hefei Cosource Medicine Technology Co. LTD., 358 Ganquan Road, Hefei, Anhui 230031, PR China
| | - Qingsong Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230036, PR China; Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230088, PR China
| | - Cai-Hong Yun
- Institute of Systems Biomedicine, Department of Biophysics, Beijing Key Laboratory of Tumor Systems Biology and Center for Molecular and Translational Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, PR China.
| | - Jing Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China.
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46
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Liang X, Lv F, Wang B, Yu K, Wu H, Qi Z, Jiang Z, Chen C, Wang A, Miao W, Wang W, Hu Z, Liu J, Liu X, Zhao Z, Wang L, Zhang S, Ye Z, Wang C, Ren T, Wang Y, Liu Q, Liu J. Discovery of 2-((3-Acrylamido-4-methylphenyl)amino)-N-(2-methyl-5-(3,4,5-trimethoxybenzamido)phenyl)-4-(methylamino)pyrimidine-5-carboxamide (CHMFL-BMX-078) as a Highly Potent and Selective Type II Irreversible Bone Marrow Kinase in the X Chromosome (BMX) Kinase Inhibitor. J Med Chem 2017; 60:1793-1816. [PMID: 28140585 DOI: 10.1021/acs.jmedchem.6b01413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BMX is a member of TEC family nonreceptor tyrosine kinase and is involved in a variety of critical physiological and pathological processes. Through combination of irreversible inhibitor design and type II inhibitor design approaches, we have discovered a highly selective and potent type II irreversible BMX kinase inhibitor compound 41 (CHMFL-BMX-078), which exhibited an IC50 of 11 nM by formation of a covalent bond with cysteine 496 residue in the DFG-out inactive conformation of BMX. It displayed a high selectivity profile (S score(1) = 0.01) against the 468 kinases/mutants in the KINOMEscan evaluation and achieved at least 40-fold selectivity over BTK kinase. Given the fact that BMX mediated signaling pathway is still not fully understood, compound 41 would serve as a useful pharmacological tool to elucidate the detailed mechanism of BMX mediated signaling pathways.
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Affiliation(s)
- Xiaofei Liang
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China
| | - Fengchao Lv
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China
| | - Beilei Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China
| | - Kailin Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China
| | - Hong Wu
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China
| | - Ziping Qi
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China
| | - Zongru Jiang
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China
| | - Cheng Chen
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China
| | - Aoli Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China
| | - Weili Miao
- Department of Chemistry, University of California-Riverside , 900 University Avenue, Riverside, California 92521, United States
| | - Wenchao Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China
| | - Zhenquan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China
| | - Juan Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China
| | - Xiaochuan Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China
| | - Zheng Zhao
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China
| | - Li Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China
| | - Shanchuan Zhang
- CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,Hefei Cosource Medicine Technology Co. Ltd. , 358 Ganquan Road, Hefei, Anhui 230031, P. R. China
| | - Zi Ye
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871, P. R. China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871, P. R. China
| | - Tao Ren
- Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei, Anhui 230088, P. R. China
| | - Yinsheng Wang
- Department of Chemistry, University of California-Riverside , 900 University Avenue, Riverside, California 92521, United States
| | - Qingsong Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,University of Science and Technology of China , Hefei, Anhui 230036, P. R. China.,Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei, Anhui 230088, P. R. China
| | - Jing Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences , Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China.,CHMFL-HCMTC Target Therapy Joint Laboratory , 350 Shushanhu Road, Hefei, Anhui 230031, P. R. China
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47
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de Wispelaere M, Carocci M, Liang Y, Liu Q, Sun E, Vetter ML, Wang J, Gray NS, Yang PL. Discovery of host-targeted covalent inhibitors of dengue virus. Antiviral Res 2016; 139:171-179. [PMID: 28034743 DOI: 10.1016/j.antiviral.2016.12.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
We report here on an approach targeting the host reactive cysteinome to identify inhibitors of host factors required for the infectious cycle of Flaviviruses and other viruses. We used two parallel cellular phenotypic screens to identify a series of covalent inhibitors, exemplified by QL-XII-47, that are active against dengue virus. We show that the compounds effectively block viral protein expression and that this inhibition is associated with repression of downstream processes of the infectious cycle, and thus significantly contributes to the potent antiviral activity of these compounds. We demonstrate that QL-XII-47's antiviral activity requires selective, covalent modification of a host target by showing that the compound's antiviral activity is recapitulated when cells are preincubated with QL-XII-47 and then washed prior to viral infection and by showing that QL-XII-47R, a non-reactive analog, lacks antiviral activity at concentrations more than 20-fold higher than QL-XII-47's IC90. QL-XII-47's inhibition of Zika virus, West Nile virus, hepatitis C virus, and poliovirus further suggests that it acts via a target mediating inhibition of these other medically relevant viruses. These results demonstrate the utility of screens targeting the host reactive cysteinome for rapid identification of compounds with potent antiviral activity.
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Affiliation(s)
| | - Margot Carocci
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yanke Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Qingsong Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eileen Sun
- Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Michael L Vetter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Priscilla L Yang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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48
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Ge Y, Jin Y, Wang C, Zhang J, Tang Z, Peng J, Liu K, Li Y, Zhou Y, Ma X. Discovery of Novel Bruton's Tyrosine Kinase (BTK) Inhibitors Bearing a N,9-Diphenyl-9 H-purin-2-amine Scaffold. ACS Med Chem Lett 2016; 7:1050-1055. [PMID: 27994736 DOI: 10.1021/acsmedchemlett.6b00235] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022] Open
Abstract
Based on the pyrimidine skeleton of EGFRT790M inhibitors, a series of N,9-diphenyl-9H-purin-2-amine derivatives were identified as effective BTK inhibitors. Among these compounds, inhibitors 10d, 10i, and 10j, possessing IC50 values of 0.5, 0.5, and 0.4 nM, displayed anti-BTK kinase activity that was as potent as the reference compounds. In particular, compound 10j suppressed the proliferation of two typical B-cell leukemia cell lines expressing high levels of BTK with concentrations of 7.75 and 12.6 μM. The activity of the subject compound as determined by the CCK-8 method and apoptosis analysis validated that inhibitor 10j is slightly more potent than AVL-292 and ibrutinib. The results of these experimental explorations suggested that 10j could serve as a valuable molecule for control of leukemia pending further developments.
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Affiliation(s)
- Yang Ge
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Yue Jin
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Changyuan Wang
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Jianbin Zhang
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Zeyao Tang
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Jinyong Peng
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Kexin Liu
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Yanxia Li
- Respiratory
Department, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, P. R. China
| | - Youwen Zhou
- Department
of Dermatology and Skin Science, University of British Columbia, Vancouver, BC V5Z 4E8, Canada
| | - Xiaodong Ma
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
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49
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Ficarro SB, Browne CM, Card JD, Alexander WM, Zhang T, Park E, McNally R, Dhe-Paganon S, Seo HS, Lamberto I, Eck MJ, Buhrlage SJ, Gray NS, Marto JA. Leveraging Gas-Phase Fragmentation Pathways for Improved Identification and Selective Detection of Targets Modified by Covalent Probes. Anal Chem 2016; 88:12248-12254. [PMID: 28193034 DOI: 10.1021/acs.analchem.6b03394] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The recent approval of covalent inhibitors for multiple clinical indications has reignited enthusiasm for this class of drugs. As interest in covalent drugs has increased, so too has the need for analytical platforms that can leverage their mechanism-of-action to characterize modified protein targets. Here we describe novel gas phase dissociation pathways which yield predictable fragment ions during MS/MS of inhibitor-modified peptides. We find that these dissociation pathways are common to numerous cysteine-directed probes as well as the covalent drugs, Ibrutinib and Neratinib. We leverage the predictable nature of these fragment ions to improve the confidence of peptide sequence assignment in proteomic analyses and explore their potential use in selective mass spectrometry-based assays.
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Affiliation(s)
- Scott B Ficarro
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Christopher M Browne
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | | | - William M Alexander
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Tinghu Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Eunyoung Park
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Randall McNally
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Sirano Dhe-Paganon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Hyuk-Soo Seo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Ilaria Lamberto
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Michael J Eck
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Sara J Buhrlage
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Jarrod A Marto
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School , Boston, Massachusetts 02115, United States
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50
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Design and synthesis of phosphoryl-substituted diphenylpyrimidines (Pho-DPPYs) as potent Bruton's tyrosine kinase (BTK) inhibitors: Targeted treatment of B lymphoblastic leukemia cell lines. Bioorg Med Chem 2016; 25:765-772. [PMID: 27956037 DOI: 10.1016/j.bmc.2016.11.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/01/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
A family of phosphoryl-substituted diphenylpyrimidine derivatives (Pho-DPPYs) were synthesized and biologically evaluated as potent BTK inhibitors in this study. Compound 7b was found to markedly inhibit BTK activity at concentrations of 0.82nmol/L, as well as to suppress the proliferations of B-cell leukemia cell lines (Ramos and Raji) expressing high levels of BTK at concentrations of 3.17μM and 6.69μM. Moreover, flow cytometry analysis results further indicated that 7b promoted cell apoptosis to a substantial degree. In a word, compound 7b is a promising BTK inhibitor for the treatment of B-cell lymphoblastic leukemia.
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