1
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Zhang H, Xu D, Huang H, Jiang H, Hu L, Liu L, Sun G, Gao J, Li Y, Xia C, Chen S, Zhou H, Kong X, Wang M, Luo C. Discovery of a Covalent Inhibitor Selectively Targeting the Autophosphorylation Site of c-Src Kinase. ACS Chem Biol 2024; 19:999-1010. [PMID: 38513196 DOI: 10.1021/acschembio.4c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Nonreceptor tyrosine kinase c-Src plays a crucial role in cell signaling and contributes to tumor progression. However, the development of selective c-Src inhibitors turns out to be challenging. In our previous study, we performed posttranslational modification-inspired drug design (PTMI-DD) to provide a plausible way for designing selective kinase inhibitors. In this study, after identifying a unique pocket comprising a less conserved cysteine and an autophosphorylation site in c-Src as well as a promiscuous covalent inhibitor, chemical optimization was performed to obtain (R)-LW-Srci-8 with nearly 75-fold improved potency (IC50 = 35.83 ± 7.21 nM). Crystallographic studies revealed the critical C-F···C═O interactions that may contribute to tight binding. The kinact and Ki values validated the improved binding affinity and decreased warhead reactivity of (R)-LW-Srci-8 for c-Src. Notably, in vitro tyrosine kinase profiling and cellular activity-based protein profiling (ABPP) cooperatively indicated a specific inhibition of c-Src by (R)-LW-Srci-8. Intriguingly, (R)-LW-Srci-8 preferentially binds to inactive c-Src with unphosphorylated Y419 both in vitro and in cells, subsequently disrupting the autophosphorylation. Collectively, our study demonstrated the feasibility of developing selective kinase inhibitors by cotargeting a nucleophilic residue and a posttranslational modification site and providing a chemical probe for c-Src functional studies.
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Affiliation(s)
- Huimin Zhang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dounan Xu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Hongchan Huang
- Center for Chemical Biology and Drug Discovery, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Hao Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Linghao Hu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
| | - Liping Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Ge Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Jing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Yuanqing Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Cuicui Xia
- Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Shijie Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Hu Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Xiangqian Kong
- Center for Chemical Biology and Drug Discovery, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Mingliang Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
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2
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Beltman RJ, Herppich AA, Bremer HJ, Pflum MKH. Affinity-Based Kinase-Catalyzed Crosslinking to Study Kinase-Substrate Pairs. Bioconjug Chem 2023; 34:1054-1060. [PMID: 37279085 PMCID: PMC10648467 DOI: 10.1021/acs.bioconjchem.3c00131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phosphorylation of proteins by kinase enzymes is a post-translational modification involved in a myriad of biological events, including cell signaling and disease development. Identifying the interactions between a kinase and its phosphorylated substrate(s) is necessary to characterize phosphorylation-mediated cellular events and encourage development of kinase-targeting drugs. One method for substrate-kinase identification utilizes photocrosslinking γ-phosphate-modified ATP analogues to covalently link kinases to their substrates for subsequent monitoring. Because photocrosslinking ATP analogues require UV light, which could influence cell biology, we report here two ATP analogues, ATP-aryl fluorosulfate (ATP-AFS) and ATP-hexanoyl bromide (ATP-HexBr), that crosslink kinase-substrate pairs via proximity-mediated reactions without the need for UV irradiation. Both ATP-AFS and ATP-HexBr acted as cosubstrates with a variety of kinases for affinity-based crosslinking, with ATP-AFS showing more robust complexes. Importantly, ATP-AFS promoted crosslinking in lysates, which demonstrates compatibility with complex cellular mixtures for future application to kinase-substrate identification.
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Affiliation(s)
- Rachel J Beltman
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Andrew A Herppich
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Hannah J Bremer
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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3
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Lu X, Smaill JB, Patterson AV, Ding K. Discovery of Cysteine-targeting Covalent Protein Kinase Inhibitors. J Med Chem 2021; 65:58-83. [PMID: 34962782 DOI: 10.1021/acs.jmedchem.1c01719] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Small molecule covalent kinase inhibitors (CKIs) have entered a new era in drug discovery, which have the advantage for sustained target inhibition and high selectivity. An increased understanding of binding kinetics of CKIs and discovery of additional irreversible and reversible-covalent cysteine-targeted warheads has inspired the development of this area. Herein, we summarize the major medicinal chemistry strategies employed in the discovery of these representative CKIs, which are categorized by the location of the target cysteine within seven main regions of the kinase: the front region, the glycine rich loop (P-loop), the hinge region, the DFG region, the activation loop (A-loop), the catalytic loop (C-loop), and the remote loop. The emphasis is placed on the design and optimization strategies of CKIs that are generated by addition of a warhead to a reversible lead/inhibitor scaffold. In addition, we address the challenges facing this area of drug discovery.
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Affiliation(s)
- Xiaoyun Lu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Adam V Patterson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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4
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Design, synthesis and biological evaluation of novel aminopyrazole- and 7-azaindole-based Nek1 inhibitors and their effects on zebrafish kidney development. Bioorg Med Chem Lett 2021; 53:128418. [PMID: 34715306 DOI: 10.1016/j.bmcl.2021.128418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 01/17/2023]
Abstract
NIMA-related protein kinase Nek1 is crucially involved in cell cycle regulation, DNA repair and microtubule regulation and dysfunctions of Nek1 play key roles in amyotrophic lateral sclerosis (ALS), polycystic kidney disease (PKD) and several types of radiotherapy resistant cancer. Targeting of Nek1 could reveal a new class of radiosensitizing substances and provide useful tools to better understand the aforementioned diseases. In this report we explore substituted aminopyrazoles and 7-azaindoles as potent inhibitors for the Nek1 kinase domain and examine their effect on kidney organogenesis in Danio rerio.
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5
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Zhang H, He J, Hu G, Zhu F, Jiang H, Gao J, Zhou H, Lin H, Wang Y, Chen K, Meng F, Hao M, Zhao K, Luo C, Liang Z. Dynamics of Post-Translational Modification Inspires Drug Design in the Kinase Family. J Med Chem 2021; 64:15111-15125. [PMID: 34668699 DOI: 10.1021/acs.jmedchem.1c01076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Post-translational modification (PTM) on protein plays important roles in the regulation of cellular function and disease pathogenesis. The systematic analysis of PTM dynamics presents great opportunities to enlarge the target space by PTM allosteric regulation. Here, we presented a framework by integrating the sequence, structural topology, and particular dynamics features to characterize the functional context and druggabilities of PTMs in the well-known kinase family. The machine learning models with these biophysical features could successfully predict PTMs. On the other hand, PTMs were identified to be significantly enriched in the reported allosteric pockets and the allosteric potential of PTM pockets were thus proposed through these biophysical features. In the end, the covalent inhibitor DC-Srci-6668 targeting the PTM pocket in c-Src kinase was identified, which inhibited the phosphorylation and locked c-Src in the inactive state. Our findings represent a crucial step toward PTM-inspired drug design in the kinase family.
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Affiliation(s)
- Huimin Zhang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China.,Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Jixiao He
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Fei Zhu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Hao Jiang
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Jing Gao
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Hu Zhou
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Hua Lin
- Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, 1 Keji Road, Fuzhou 350117, China
| | - Yingjuan Wang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Kaixian Chen
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Fanwang Meng
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Minghong Hao
- Ensem Therapeutics, Inc., 200 Boston Avenue, Medford, Massachusetts 02155, United States
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
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6
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Structural insights into redox-active cysteine residues of the Src family kinases. Redox Biol 2021; 41:101934. [PMID: 33765616 PMCID: PMC8022254 DOI: 10.1016/j.redox.2021.101934] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/18/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
The Src Family Kinases (SFKs) are pivotal regulators of cellular signal transduction and highly sought-after targets in drug discovery. Their actions within cells are controlled by alterations in protein phosphorylation that switch the SFKs from autoinhibited to active states. The SFKs are also well recognized to contain redox-active cysteine residues where oxidation of certain residues directly contribute to kinase function. To more completely understand the factors that influence cysteine oxidation within the SFKs, a review is presented of the local structural environments surrounding SFK cysteine residues compared to their quantified oxidation in vivo from the Oximouse database. Generally, cysteine local structure and degree of redox sensitivity vary with respect to sequence conservation. Cysteine residues found in conserved positions are more mildly redox-active as they are found in hydrophobic environments and not fully exposed to solvent. Non-conserved redox-active cysteines are generally the most reactive with direct solvent access and/or in hydrophilic environments. Results from this analysis motivate future efforts to conduct comprehensive proteome-wide analysis of redox-sensitivity, conservation, and local structural environments of proteins containing reactive cysteine residues.
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7
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Lee S, Kim J, Jo J, Chang JW, Sim J, Yun H. Recent advances in development of hetero-bivalent kinase inhibitors. Eur J Med Chem 2021; 216:113318. [PMID: 33730624 DOI: 10.1016/j.ejmech.2021.113318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
Abstract
Identifying a pharmacological agent that targets only one of more than 500 kinases present in humans is an important challenge. One potential solution to this problem is the development of bivalent kinase inhibitors, which consist of two connected fragments, each bind to a dissimilar binding site of the bisubstrate enzyme. The main advantage of bivalent (type V) kinase inhibitors is generating more interactions with target enzymes that can enhance the molecules' selectivity and affinity compared to single-site inhibitors. Earlier type V inhibitors were not suitable for the cellular environment and were mostly used in in vitro studies. However, recently developed bivalent compounds have high kinase affinity, high biological and chemical stability in vivo. This review summarized the hetero-bivalent kinase inhibitors described in the literature from 2014 to the present. We attempted to classify the molecules by serine/threonine and tyrosine kinase inhibitors, and then each target kinase and its hetero-bivalent inhibitor was assessed in depth. In addition, we discussed the analysis of advantages, limitations, and perspectives of bivalent kinase inhibitors compared with the monovalent kinase inhibitors.
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Affiliation(s)
- Seungbeom Lee
- College of Pharmacy, CHA University, Pocheon-si, Gyeonggi-do, 11160, Republic of Korea
| | - Jisu Kim
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jeyun Jo
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jae Won Chang
- Department of Pharmacology & Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Department of Hematology & Medical Oncology, School of Medicine, Emory University, Atlanta, GA, USA; Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Jaehoon Sim
- College of Pharmacy, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea.
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8
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Chakraborty MP, Bhattacharyya S, Roy S, Bhattacharya I, Das R, Mukherjee A. Selective targeting of the inactive state of hematopoietic cell kinase (Hck) with a stable curcumin derivative. J Biol Chem 2021; 296:100449. [PMID: 33617879 PMCID: PMC7946438 DOI: 10.1016/j.jbc.2021.100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/05/2021] [Accepted: 02/18/2021] [Indexed: 11/29/2022] Open
Abstract
Hck, a Src family nonreceptor tyrosine kinase (SFK), has recently been established as an attractive pharmacological target to improve pulmonary function in COVID-19 patients. Hck inhibitors are also well known for their regulatory role in various malignancies and autoimmune diseases. Curcumin has been previously identified as an excellent DYRK-2 inhibitor, but curcumin's fate is tainted by its instability in the cellular environment. Besides, small molecules targeting the inactive states of a kinase are desirable to reduce promiscuity. Here, we show that functionalization of the 4-arylidene position of the fluorescent curcumin scaffold with an aryl nitrogen mustard provides a stable Hck inhibitor (Kd = 50 ± 10 nM). The mustard curcumin derivative preferentially interacts with the inactive conformation of Hck, similar to type-II kinase inhibitors that are less promiscuous. Moreover, the lead compound showed no inhibitory effect on three other kinases (DYRK2, Src, and Abl). We demonstrate that the cytotoxicity may be mediated via inhibition of the SFK signaling pathway in triple-negative breast cancer and murine macrophage cells. Our data suggest that curcumin is a modifiable fluorescent scaffold to develop selective kinase inhibitors by remodeling its target affinity and cellular stability.
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Affiliation(s)
- Manas Pratim Chakraborty
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India
| | - Sudipta Bhattacharyya
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India
| | - Souryadip Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India
| | - Indira Bhattacharya
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India
| | - Rahul Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India; Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India.
| | - Arindam Mukherjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India; Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India.
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9
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Gurbani D, Du G, Henning NJ, Rao S, Bera AK, Zhang T, Gray NS, Westover KD. Structure and Characterization of a Covalent Inhibitor of Src Kinase. Front Mol Biosci 2020; 7:81. [PMID: 32509799 PMCID: PMC7248381 DOI: 10.3389/fmolb.2020.00081] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/08/2020] [Indexed: 12/11/2022] Open
Abstract
Unregulated Src activity promotes malignant processes in cancer, but no Src-directed targeted therapies are used clinically, possibly because early Src inhibitors produce off-target effects leading to toxicity. Improved selective Src inhibitors may enable Src-directed therapies. Previously, we reported an irreversible Src inhibitor, DGY-06-116, based on the hybridization of dasatinib and a promiscuous covalent kinase probe SM1-71. Here, we report biochemical and biophysical characterization of this compound. An x-ray co-crystal structure of DGY-06-116: Src shows a covalent interaction with the kinase p-loop and occupancy of the back hydrophobic kinase pocket, explaining its high potency, and selectivity. However, a reversible analog also shows similar potency. Kinetic analysis shows a slow inactivation rate compared to other clinically approved covalent kinase inhibitors, consistent with a need for p-loop movement prior to covalent bond formation. Overall, these results suggest that a strong reversible interaction is required to allow sufficient time for the covalent reaction to occur. Further optimization of the covalent linker may improve the kinetics of covalent bond formation.
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Affiliation(s)
- Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, United States
| | - Guangyan Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Nathaniel J. Henning
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Suman Rao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
- Harvard Program in Therapeutic Science (HiTS), Harvard Medical School, Boston, MA, United States
| | - Asim K. Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, United States
| | - Tinghu Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Nathanael S. Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Kenneth D. Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, United States
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10
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Manda S, Lee NK, Oh DC, Lee J. Design, Synthesis, and Biological Evaluation of Proteolysis Targeting Chimeras (PROTACs) for the Dual Degradation of IGF-1R and Src. Molecules 2020; 25:molecules25081948. [PMID: 32340152 PMCID: PMC7221895 DOI: 10.3390/molecules25081948] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 01/28/2023] Open
Abstract
A focused PROTAC library was developed to degrade both IGF-1R and Src proteins, which are associated with various cancers. PROTACs with IGF-1R and Src degradation potentials were synthesized by tethering different inhibitor warhead units and the E3 ligase (CRBN) recruiting-pomalidomide with various linkers. The designed PROTACs 12a-b inhibited the proliferation and migration of MCF7 and A549 cancer cells with low micromolar potency (1-5 μM) in various cellular assays.
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Affiliation(s)
- Sudhakar Manda
- College of Pharmacy, Research Institute of Pharmaceutical sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (S.M.); (N.K.L.)
| | - Na Keum Lee
- College of Pharmacy, Research Institute of Pharmaceutical sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (S.M.); (N.K.L.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea;
| | - Jeeyeon Lee
- College of Pharmacy, Research Institute of Pharmaceutical sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (S.M.); (N.K.L.)
- Correspondence: ; Tel.: +82-02-880-2471
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11
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Du G, Rao S, Gurbani D, Henning NJ, Jiang J, Che J, Yang A, Ficarro SB, Marto JA, Aguirre AJ, Sorger PK, Westover KD, Zhang T, Gray NS. Structure-Based Design of a Potent and Selective Covalent Inhibitor for SRC Kinase That Targets a P-Loop Cysteine. J Med Chem 2020; 63:1624-1641. [PMID: 31935084 PMCID: PMC7493195 DOI: 10.1021/acs.jmedchem.9b01502] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SRC is a major regulator of many signaling pathways and contributes to cancer development. However, development of a selective SRC inhibitor has been challenging, and FDA-approved SRC inhibitors, dasatinib and bosutinib, are multitargeted kinase inhibitors. Here, we describe our efforts to develop a selective SRC covalent inhibitor by targeting cysteine 277 on the P-loop of SRC. Using a promiscuous covalent kinase inhibitor (CKI) SM1-71 as a starting point, we developed covalent inhibitor 15a, which discriminates SRC from other covalent targets of SM1-71 including TAK1 and FGFR1. As an irreversible covalent inhibitor, compound 15a exhibited sustained inhibition of SRC signaling both in vitro and in vivo. Moreover, 15a exhibited potent antiproliferative effects in nonsmall cell lung cancer cell lines harboring SRC activation, thus providing evidence that this approach may be promising for further drug development efforts.
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Affiliation(s)
- Guangyan Du
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
- Department of Cancer Biology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Suman Rao
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
- Department of Cancer Biology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
- Laboratory of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology , The University of Texas Southwestern Medical Center at Dallas , Dallas , Texas 75390 , United States
| | - Nathaniel J Henning
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
- Department of Cancer Biology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Jie Jiang
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
- Department of Cancer Biology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Jianwei Che
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
- Department of Cancer Biology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Annan Yang
- Department of Medical Oncology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Scott B Ficarro
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Jarrod A Marto
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Andrew J Aguirre
- Department of Medical Oncology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Peter K Sorger
- Laboratory of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology , The University of Texas Southwestern Medical Center at Dallas , Dallas , Texas 75390 , United States
| | - Tinghu Zhang
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
- Department of Cancer Biology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
- Department of Cancer Biology , Dana Farber Cancer Institute , 450 Brookline Avenue , Boston , Massachusetts 02215 , United States
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12
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Agius MP, Ko KS, Johnson TK, Kwarcinski FE, Phadke S, Lachacz EJ, Soellner MB. Selective Proteolysis to Study the Global Conformation and Regulatory Mechanisms of c-Src Kinase. ACS Chem Biol 2019; 14:1556-1563. [PMID: 31287657 PMCID: PMC7254491 DOI: 10.1021/acschembio.9b00306] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein kinase pathways are traditionally mapped by monitoring downstream phosphorylation. Meanwhile, the noncatalytic functions of protein kinases remain under-appreciated as critical components of kinase signaling. c-Src is a protein kinase known to have noncatalytic signaling function important in healthy and disease cell signaling. Large conformational changes in the regulatory domains regulate c-Src's noncatalytic functions. Herein, we demonstrate that changes in the global conformation of c-Src can be monitored using a selective proteolysis methodology. Further, we use this methodology to investigate changes in the global conformation of several clinical and nonclinical mutations of c-Src. Significantly, we identify a novel activating mutation observed clinically, W121R, that can escape down-regulation mechanisms. Our methodology can be expanded to monitor the global conformation of other tyrosine kinases, including c-Abl, and represents an important tool toward the elucidation of the noncatalytic functions of protein kinases.
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Affiliation(s)
- Michael P. Agius
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI
| | - Kristin S. Ko
- Department of Chemistry, University of Michigan, Ann Arbor, MI
| | - Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI
| | | | - Sameer Phadke
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Eric J. Lachacz
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Matthew B. Soellner
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
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13
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Rao S, Gurbani D, Du G, Everley RA, Browne CM, Chaikuad A, Tan L, Schröder M, Gondi S, Ficarro SB, Sim T, Kim ND, Berberich MJ, Knapp S, Marto JA, Westover KD, Sorger PK, Gray NS. Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome. Cell Chem Biol 2019; 26:818-829.e9. [PMID: 30982749 PMCID: PMC6634314 DOI: 10.1016/j.chembiol.2019.02.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/18/2018] [Accepted: 02/27/2019] [Indexed: 12/30/2022]
Abstract
Covalent kinase inhibitors, which typically target cysteine residues, represent an important class of clinically relevant compounds. Approximately 215 kinases are known to have potentially targetable cysteines distributed across 18 spatially distinct locations proximal to the ATP-binding pocket. However, only 40 kinases have been covalently targeted, with certain cysteine sites being the primary focus. To address this disparity, we have developed a strategy that combines the use of a multi-targeted acrylamide-modified inhibitor, SM1-71, with a suite of complementary chemoproteomic and cellular approaches to identify additional targetable cysteines. Using this single multi-targeted compound, we successfully identified 23 kinases that are amenable to covalent inhibition including MKNK2, MAP2K1/2/3/4/6/7, GAK, AAK1, BMP2K, MAP3K7, MAPKAPK5, GSK3A/B, MAPK1/3, SRC, YES1, FGFR1, ZAK (MLTK), MAP3K1, LIMK1, and RSK2. The identification of nine of these kinases previously not targeted by a covalent inhibitor increases the number of targetable kinases and highlights opportunities for covalent kinase inhibitor development.
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Affiliation(s)
- Suman Rao
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Guangyan Du
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Everley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher M Browne
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany
| | - Li Tan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Martin Schröder
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Taebo Sim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Nam Doo Kim
- NDBio Therapeutics Inc., Incheon 21984, Republic of Korea
| | - Matthew J Berberich
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; German Cancer Network (DKTK), Frankfurt Site, 60438 Frankfurt am Main, Germany
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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14
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Abstract
Kinase inhibitors (KIs) have had a huge impact on clinical treatment of various cancers, but they are far from perfect medicines. In particular, their efficacies are limited to certain cancer types and, in many cases, provide only temporary remission. This paper explores the possibility of covalently binding a fluorophore for in vivo optical imaging to the KI dasatinib where the particular fluorophore chosen for this study, a heptamethine cyanine (Cy) derivative, tends to accumulate in tumors. Thus, we hypothesized that the dasatinib-fluorophore conjugate might target tumor cells more effectively than the parent KI, give enhanced suppression of viability, and simultaneously serve as a probe for optical imaging. As far as we are aware, the dasatinib conjugate (1) is the first reported to contain this KI and a probe for near-IR imaging, and it is certainly the first conjugate of a tumor-targeting near-IR dye and a KI of any kind. Conjugate 1 suppressed the viability of liver cancer cells (HepG2) more effectively than dasatinib at the same concentration. In scratch assays, 1 prevented regrowth of the tumor cells. Conjugate 1 is cell permeable, and confocal imaging indicates the fluorescence of those cells is concentrated in the mitochondria than lysosomes. In general, this study suggests there is untapped potential for conjugates of KIs with tumor-targeting near-IR dyes in the development of theranostics for optical imaging and treatment of cancer.
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Affiliation(s)
- Syed Muhammad Usama
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Bosheng Zhao
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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15
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Harris CM, Foley SE, Goedken ER, Michalak M, Murdock S, Wilson NS. Merits and Pitfalls in the Characterization of Covalent Inhibitors of Bruton's Tyrosine Kinase. SLAS DISCOVERY 2018; 23:1040-1050. [PMID: 29991334 DOI: 10.1177/2472555218787445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In vitro analysis of covalent inhibitors requires special consideration, due to the time-dependent and typically irreversible nature of their target interaction. While many analyses are reported for the characterization of a final candidate, it is less clear which are most useful in the lead optimization phase of drug discovery. In the context of identifying covalent inhibitors of Bruton's tyrosine kinase (BTK), we evaluated multiple techniques for characterizing covalent inhibitors. Several methods qualitatively support the covalent mechanism of action or support a particular aspect of interaction but were not otherwise informative to differentiate inhibitors. These include the time dependence of IC50, substrate competition, mass spectrometry, and recovery of function after inhibitor removal at the biochemical and cellular level. A change in IC50 upon mutation of the targeted BTK C481 nucleophile or upon removal of the electrophilic moiety of the inhibitor was not always a reliable indicator of covalent inhibition. Determination of kinact and KI provides a quantitative description of covalent interactions but was challenging at scale and frequently failed to provide more than the ratio of the two values, kinact/KI. Overall, a combination of approaches is required to assess time-dependent, covalent, and irreversible inhibitors in a manner suitable to reliably advance drug candidates.
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Affiliation(s)
| | - Sage E Foley
- 2 Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Eric R Goedken
- 3 Foundational Immunology, AbbVie Bioresearch Center, Worcester, MA, USA
| | - Mark Michalak
- 4 Protein Sciences, AbbVie Bioresearch Center, Worcester, MA, USA
| | - Sara Murdock
- 1 Immunology Pharmacology, AbbVie Bioresearch Center, Worcester, MA, USA
| | - Noel S Wilson
- 5 Discovery Chemistry and Technology, AbbVie, North Chicago, IL, USA
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16
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Xu Y, Cuccui J, Denman C, Maharjan T, Wren BW, Wagner GK. Structure-activity relationships in a new class of non-substrate-like covalent inhibitors of the bacterial glycosyltransferase LgtC. Bioorg Med Chem 2018; 26:2973-2983. [PMID: 29602676 DOI: 10.1016/j.bmc.2018.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/03/2018] [Accepted: 03/04/2018] [Indexed: 02/07/2023]
Abstract
Lipooligosaccharide (LOS) structures in the outer core of Gram-negative mucosal pathogens such as Neisseria meningitidis and Haemophilus influenzae contain characteristic glycoepitopes that contribute significantly to bacterial virulence. An important example is the digalactoside epitope generated by the retaining α-1,4-galactosyltransferase LgtC. These digalactosides camouflage the pathogen from the host immune system and increase its serum resistance. Small molecular inhibitors of LgtC are therefore sought after as chemical tools to study bacterial virulence, and as potential candidates for anti-virulence drug discovery. We have recently discovered a new class of non-substrate-like inhibitors of LgtC. The new inhibitors act via a covalent mode of action, targeting a non-catalytic cysteine residue in the LgtC active site. Here, we describe, for the first time, structure-activity relationships for this new class of glycosyltransferase inhibitors. We have carried out a detailed analysis of the inhibition kinetics to establish the relative contribution of the non-covalent binding and the covalent inactivation steps for overall inhibitory activity. Selected inhibitors were also evaluated against a serum-resistant strain of Haemophilus influenzae, but did not enhance the killing effect of human serum.
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Affiliation(s)
- Yong Xu
- King's College London, Department of Chemistry, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Jon Cuccui
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, UK
| | - Carmen Denman
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, UK
| | - Tripty Maharjan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, UK
| | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, UK
| | - Gerd K Wagner
- King's College London, Department of Chemistry, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
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17
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Pettinger J, Jones K, Cheeseman MD. Lysine-Targeting Covalent Inhibitors. Angew Chem Int Ed Engl 2017; 56:15200-15209. [PMID: 28853194 DOI: 10.1002/anie.201707630] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/23/2017] [Indexed: 12/11/2022]
Abstract
Targeted covalent inhibitors have gained widespread attention in drug discovery as a validated method to circumvent acquired resistance in oncology. This strategy exploits small-molecule/protein crystal structures to design tightly binding ligands with appropriately positioned electrophilic warheads. Whilst most focus has been on targeting binding-site cysteine residues, targeting nucleophilic lysine residues can also represent a viable approach to irreversible inhibition. However, owing to the basicity of the ϵ-amino group in lysine, this strategy generates a number of specific challenges. Herein, we review the key principles for inhibitor design, give historical examples, and present recent developments that demonstrate the potential of lysine targeting for future drug discovery.
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Keith Jones
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Matthew D Cheeseman
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
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18
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
| | - Keith Jones
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
| | - Matthew D. Cheeseman
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
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19
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Heppner DE, Hristova M, Dustin CM, Danyal K, Habibovic A, van der Vliet A. The NADPH Oxidases DUOX1 and NOX2 Play Distinct Roles in Redox Regulation of Epidermal Growth Factor Receptor Signaling. J Biol Chem 2016; 291:23282-23293. [PMID: 27650496 DOI: 10.1074/jbc.m116.749028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Indexed: 12/31/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) plays a critical role in regulating airway epithelial homeostasis and responses to injury. Activation of EGFR is regulated by redox-dependent processes involving reversible cysteine oxidation by reactive oxygen species (ROS) and involves both ligand-dependent and -independent mechanisms, but the precise source(s) of ROS and the molecular mechanisms that control tyrosine kinase activity are incompletely understood. Here, we demonstrate that stimulation of EGFR activation by ATP in airway epithelial cells is closely associated with dynamic reversible oxidation of cysteine residues via sequential sulfenylation and S-glutathionylation within EGFR and the non-receptor-tyrosine kinase Src. Moreover, the intrinsic kinase activity of recombinant Src or EGFR was in both cases enhanced by H2O2 but not by GSSG, indicating that the intermediate sulfenylation is the activating modification. H2O2-induced increase in EGFR tyrosine kinase activity was not observed with the C797S variant, confirming Cys-797 as the redox-sensitive cysteine residue that regulates kinase activity. Redox-dependent regulation of EGFR activation in airway epithelial cells was found to strongly depend on activation of either the NADPH oxidase DUOX1 or the homolog NOX2, depending on the activation mechanism. Whereas DUOX1 and Src play a primary role in EGFR transactivation by wound-derived signals such as ATP, direct ligand-dependent EGFR activation primarily involves NOX2 with a secondary role for DUOX1 and Src. Collectively, our findings establish that redox-dependent EGFR kinase activation involves a dynamic and reversible cysteine oxidation mechanism and that this activation mechanism variably involves DUOX1 and NOX2.
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Affiliation(s)
- David E Heppner
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Milena Hristova
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Christopher M Dustin
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Karamatullah Danyal
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Aida Habibovic
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Albert van der Vliet
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
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20
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Danyal K, de Jong W, O'Brien E, Bauer RA, Heppner DE, Little AC, Hristova M, Habibovic A, van der Vliet A. Acrolein and thiol-reactive electrophiles suppress allergen-induced innate airway epithelial responses by inhibition of DUOX1 and EGFR. Am J Physiol Lung Cell Mol Physiol 2016; 311:L913-L923. [PMID: 27612966 DOI: 10.1152/ajplung.00276.2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/05/2016] [Indexed: 01/27/2023] Open
Abstract
Acrolein is a major thiol-reactive component of cigarette smoke (CS) that is thought to contribute to increased asthma incidence associated with smoking. Here, we explored the effects of acute acrolein exposure on innate airway responses to two common airborne allergens, house dust mite and Alternaria alternata, and observed that acrolein exposure of C57BL/6 mice (5 ppm, 4 h) dramatically inhibited innate airway responses to subsequent allergen challenge, demonstrated by attenuated release of the epithelial-derived cytokines IL-33, IL-25, and IL-1α. Acrolein and other anti-inflammatory thiol-reactive electrophiles, cinnamaldehyde, curcumin, and sulforaphane, similarly inhibited allergen-induced production of these cytokines from human or murine airway epithelial cells in vitro. Based on our previous observations indicating the importance of Ca2+-dependent signaling, activation of the NADPH oxidase DUOX1, and Src/EGFR-dependent signaling in allergen-induced epithelial secretion of these cytokines, we explored the impact of acrolein on these pathways. Acrolein and other thiol-reactive electrophiles were found to dramatically prevent allergen-induced activation of DUOX1 as well as EGFR, and acrolein was capable of inhibiting EGFR tyrosine kinase activity via modification of C797. Biotin-labeling strategies indicated increased cysteine modification and carbonylation of Src, EGFR, as well as DUOX1, in response to acrolein exposure in vitro and in vivo, suggesting that direct alkylation of these proteins on accessible cysteine residues may be responsible for their inhibition. Collectively, our findings indicate a novel anti-inflammatory mechanism of CS-derived acrolein and other thiol-reactive electrophiles, by directly inhibiting DUOX1- and EGFR-mediated airway epithelial responses to airborne allergens.
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Affiliation(s)
- Karamatullah Danyal
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
| | - Willem de Jong
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
| | - Edmund O'Brien
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
| | - Robert A Bauer
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
| | - David E Heppner
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
| | - Andrew C Little
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
| | - Aida Habibovic
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, Vermont
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21
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Aleem S, Georghiou G, Kleiner RE, Guja K, Craddock BP, Lyczek A, Chan AI, Garcia-Diaz M, Miller WT, Liu DR, Seeliger MA. Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles. Cell Chem Biol 2016; 23:1103-1112. [PMID: 27593110 DOI: 10.1016/j.chembiol.2016.07.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 07/04/2016] [Accepted: 07/14/2016] [Indexed: 12/12/2022]
Abstract
Protein kinases are attractive therapeutic targets because their dysregulation underlies many diseases, including cancer. The high conservation of the kinase domain and the evolution of drug resistance, however, pose major challenges to the development of specific kinase inhibitors. We recently discovered selective Src kinase inhibitors from a DNA-templated macrocycle library. Here, we reveal the structural basis for how these inhibitors retain activity against a disease-relevant, drug-resistant kinase mutant, while maintaining Src specificity. We find that these macrocycles display a degree of modularity: two of their three variable groups interact with sites on the kinase that confer selectivity, while the third group interacts with the universally conserved catalytic lysine and thereby retains the ability to inhibit the "gatekeeper" kinase mutant. We also show that these macrocycles inhibit migration of MDA-MB-231 breast tumor cells. Our findings establish intracellular kinase inhibition by peptidic macrocycles, and inform the development of potent and specific kinase inhibitors.
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Affiliation(s)
- Saadat Aleem
- Dept. of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - George Georghiou
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Ralph E Kleiner
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kip Guja
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Barbara P Craddock
- Dept. of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Agatha Lyczek
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Alix I Chan
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Miguel Garcia-Diaz
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - W Todd Miller
- Dept. of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - David R Liu
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Markus A Seeliger
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
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22
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Baillie TA. Targeted Covalent Inhibitors for Drug Design. Angew Chem Int Ed Engl 2016; 55:13408-13421. [DOI: 10.1002/anie.201601091] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Thomas A. Baillie
- Department of Medicinal Chemistry, School of Pharmacy; University of Washington; Box 357610 Seattle WA 98195-7610 USA
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23
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Affiliation(s)
- Thomas A. Baillie
- Department of Medicinal Chemistry, School of Pharmacy; University of Washington; Box 357610 Seattle WA 98195-7610 USA
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24
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Abstract
We have developed a general methodology to produce bivalent kinase inhibitors for c-Src that interact with the SH2 and ATP binding pockets. Our approach led to a highly selective bivalent inhibitor of c-Src. We demonstrate impressive selectivity for c-Src over homologous kinases. Exploration of the unexpected high level of selectivity yielded insight into the inherent flexibility of homologous kinases. Finally, we demonstrate that our methodology is modular and both the ATP-competitive fragment and conjugation chemistry can be swapped.
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Affiliation(s)
- Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Matthew B. Soellner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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25
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Kwarcinski FE, Steffey ME, Fox CC, Soellner MB. Discovery of Bivalent Kinase Inhibitors via Enzyme-Templated Fragment Elaboration. ACS Med Chem Lett 2015; 6:898-901. [PMID: 26286460 DOI: 10.1021/acsmedchemlett.5b00167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/13/2015] [Indexed: 11/29/2022] Open
Abstract
We have employed novel fragment-based screening methodology to discover bivalent kinase inhibitors with improved selectivity. Starting from a low molecular weight promiscuous kinase inhibitor, we appended a thiol for subsequent reaction with a library of acrylamide electrophiles. Enzyme-templated screening was performed to identify acrylamides that assemble into bivalent inhibitors of c-Src kinase. Upon identification of acrylamide fragments that improve the binding affinity of our lead thiol, we characterized the resulting bivalent inhibitors and identified a series of kinase inhibitors with improved potency and selectivity compared to the thiol-containing precursor. Provided that protein can be prepared free of endogenous reactive cysteines, our methodology is general and could be applied to nearly any enzyme of interest.
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Affiliation(s)
- Frank E. Kwarcinski
- Departments of †Medicinal Chemistry and ‡Chemistry, University of Michigan, 930 North
University Avenue, Ann Arbor, Michigan 48109, United States
| | - Michael E. Steffey
- Departments of †Medicinal Chemistry and ‡Chemistry, University of Michigan, 930 North
University Avenue, Ann Arbor, Michigan 48109, United States
| | - Christel C. Fox
- Departments of †Medicinal Chemistry and ‡Chemistry, University of Michigan, 930 North
University Avenue, Ann Arbor, Michigan 48109, United States
| | - Matthew B. Soellner
- Departments of †Medicinal Chemistry and ‡Chemistry, University of Michigan, 930 North
University Avenue, Ann Arbor, Michigan 48109, United States
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26
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Larraufie MH, Yang WS, Jiang E, Thomas AG, Slusher BS, Stockwell BR. Incorporation of metabolically stable ketones into a small molecule probe to increase potency and water solubility. Bioorg Med Chem Lett 2015; 25:4787-4792. [PMID: 26231156 DOI: 10.1016/j.bmcl.2015.07.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 12/21/2022]
Abstract
Introducing a reactive carbonyl to a scaffold that does not otherwise have an electrophilic functionality to create a reversible covalent inhibitor is a potentially useful strategy for enhancing compound potency. However, aldehydes are metabolically unstable, which precludes the use of this strategy for compounds to be tested in animal models or in human clinical studies. To overcome this limitation, we designed ketone-based functionalities capable of forming reversible covalent adducts, while displaying high metabolic stability, and imparting improved water solubility to their pendant scaffold. We tested this strategy on the ferroptosis inducer and experimental therapeutic erastin, and observed substantial increases in compound potency. In particular, a new carbonyl erastin analog, termed IKE, displayed improved potency, solubility and metabolic stability, thus representing an ideal candidate for future in vivo cancer therapeutic applications.
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Affiliation(s)
- Marie-Helene Larraufie
- Department of Biological Sciences, Columbia University, 550 West 120th Street, 1208 Northwest Corner Building, MC 4846, New York, NY 10027, United States
| | - Wan Seok Yang
- Department of Biological Sciences, Columbia University, 550 West 120th Street, 1208 Northwest Corner Building, MC 4846, New York, NY 10027, United States
| | - Elise Jiang
- Department of Chemistry, Columbia University, New York, NY 10027, United States
| | - Ajit G Thomas
- Brain Science Institute, Johns Hopkins Medicine, Baltimore, United States
| | - Barbara S Slusher
- Brain Science Institute, Johns Hopkins Medicine, Baltimore, United States; Department of Neurology, Johns Hopkins Medicine, Baltimore, United States
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, 550 West 120th Street, 1208 Northwest Corner Building, MC 4846, New York, NY 10027, United States; Department of Chemistry, Columbia University, New York, NY 10027, United States; Howard Hughes Medical Institute, Columbia University, New York, NY 10027, United States.
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27
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Zhang CH, Zheng MW, Li YP, Lin XD, Huang M, Zhong L, Li GB, Zhang RJ, Lin WT, Jiao Y, Wu XA, Yang J, Xiang R, Chen LJ, Zhao YL, Cheng W, Wei YQ, Yang SY. Design, Synthesis, and Structure–Activity Relationship Studies of 3-(Phenylethynyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine Derivatives as a New Class of Src Inhibitors with Potent Activities in Models of Triple Negative Breast Cancer. J Med Chem 2015; 58:3957-74. [PMID: 25835317 DOI: 10.1021/acs.jmedchem.5b00270] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Chun-Hui Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Ming-Wu Zheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Ya-Ping Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Xing-Dong Lin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Mei Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Lei Zhong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Guo-Bo Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Rong-Jie Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Wan-Ting Lin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Yan Jiao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Xiao-Ai Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Jiao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Rong Xiang
- Department of Clinical
Medicine, School of Medicine, Nankai University, Tianjin 300071, China
| | - Li-Juan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Ying-Lan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Wei Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Yu-Quan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Sheng-Yong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative
Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
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28
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Hwang CS, Kung A, Kashemirov BA, Zhang C, McKenna CE. 5'-β,γ-CHF-ATP diastereomers: synthesis and fluorine-mediated selective binding by c-Src protein kinase. Org Lett 2015; 17:1624-7. [PMID: 25781066 PMCID: PMC4892180 DOI: 10.1021/ol503765n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The first preparation of the individual β,γ-CHF-ATP stereoisomers 12a and 12b is reported. Configurationally differing solely by the orientation of the C-F fluorine, 12a and 12b have discrete (31)P (202 MHz, pH 10.9, ΔδPα 6 Hz, ΔδPβ 4 Hz) and (19)F NMR (470 MHz, pH 9.8, ΔδF 25 Hz) spectral signatures and exhibit a 6-fold difference in IC50 values for c-Src kinase, attributed to a unique interaction of the (S)-fluorine of bound 12b with R388 in the active site.
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Affiliation(s)
- Candy S. Hwang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Alvin Kung
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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29
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Abstract
A key issue in drug discovery is how to reduce drug dosage and increase specificity while retaining or increasing efficacy, as high dosage is often linked to toxicity. There are two types of drugs on the market: orthosteric and allosteric. Orthosteric drugs can be noncovalent or covalent. The latter are advantageous because they may be prescribed in lower doses, but their potential off-target toxicity is a primary concern. The chief advantages of allosteric drugs are their higher specificity and their consequently lower chance of toxic side effects. Covalent allosteric drugs combine the pharmacological merits of covalent drugs with the additional benefit of the higher specificity of allosteric drugs. In a recent promising step in therapeutic drug development, allosteric, disulfide-tethered fragments successfully modulated the activity of a protein kinase and K-Ras.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702;
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30
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Li X, Zuo Y, Tang G, Wang Y, Zhou Y, Wang X, Guo T, Xia M, Ding N, Pan Z. Discovery of a Series of 2,5-Diaminopyrimidine Covalent Irreversible Inhibitors of Bruton’s Tyrosine Kinase with in Vivo Antitumor Activity. J Med Chem 2014; 57:5112-28. [DOI: 10.1021/jm4017762] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xitao Li
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yingying Zuo
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Guanghui Tang
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yan Wang
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yiqing Zhou
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Xueying Wang
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Tianlin Guo
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Mengying Xia
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Ning Ding
- Key Laboratory of Carcinogenesis and Translational Research (Ministry
of Education), Department of Lymphoma, Peking University Cancer Hospital and Institute, No. 52 Fucheng Road, Haidian
District, Beijing, 100142, China
| | - Zhengying Pan
- Key Laboratory of
Chemical Genomics, Key Laboratory of Structural Biology, School of
Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
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31
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Rauh D. A special thematic compilation/special issue crossover with Biochemistry, Journal of Medicinal Chemistry, and ACS Medicinal Chemistry Letters focused on kinases. ACS Chem Biol 2014; 9:579-80. [PMID: 24650390 DOI: 10.1021/cb500150d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Arian D, Hedayati M, Zhou H, Bilis Z, Chen K, DeWeese TL, Greenberg MM. Irreversible inhibition of DNA polymerase β by small-molecule mimics of a DNA lesion. J Am Chem Soc 2014; 136:3176-83. [PMID: 24517090 DOI: 10.1021/ja411733s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Abasic sites are ubiquitous DNA lesions that are mutagenic and cytotoxic but are removed by the base excision repair pathway. DNA polymerase β carries out two of the four steps during base excision repair, including a lyase reaction that removes the abasic site from DNA following incision of its 5'-phosphate. DNA polymerase β is overexpressed in cancer cells and is a potential anticancer target. Recently, DNA oxidized abasic sites that are produced by potent antitumor agents were shown to inactivate DNA polymerase β. A library of small molecules whose structures were inspired by the oxidized abasic sites was synthesized and screened for the ability to irreversibly inhibit DNA polymerase β. One candidate (3a) was examined more thoroughly, and modification of its phosphate backbone led to a molecule that irreversibly inactivates DNA polymerase β in solution (IC50 ≈ 21 μM), and inhibits the enzyme's lyase activity in cell lysates. A bisacetate analogue is converted in cell lysates to 3a. The bisacetate is more effective in cell lysates, more cytotoxic in prostate cancer cells than 3a and potentiates the cytotoxicity of methyl methanesulfonate between 2- and 5-fold. This is the first example of an irreversible inhibitor of the lyase activity of DNA polymerase β that works synergistically with a DNA damaging agent.
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Affiliation(s)
- Dumitru Arian
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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33
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Cheng X, Li L, Uttamchandani M, Yao SQ. A tuned affinity-based staurosporine probe for in situ profiling of protein kinases. Chem Commun (Camb) 2014; 50:2851-3. [PMID: 24496501 DOI: 10.1039/c4cc00184b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A clickable and cell-permeable affinity-based probe (AfBP) was designed from staurosporine, by incorporating an electrophilic chloroacetamide warhead to facilitate in situ proteome labeling of a range of potential kinase targets.
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Affiliation(s)
- Xiamin Cheng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore117543.
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34
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Abstract
Protein kinase inhibitors are an important class of therapeutics. In addition, selective kinase inhibitors can often reveal unexpected biological insights, augmenting genetic approaches and playing a decisive role in preclinical target validation studies. Nevertheless, developing protein kinase inhibitors with sufficient selectivity and pharmacodynamic potency presents significant challenges. Targeting noncatalytic cysteines with covalent inhibitors is a powerful approach to address both challenges simultaneously. Here, we describe our efforts to design irreversible and reversible electrophilic inhibitors with varying degrees of kinase selectivity. Highly selective covalent inhibitors have been used to elucidate the roles of p90 ribosomal protein S6 kinases in animal models of atherosclerosis and diabetes. By contrast, semipromiscuous covalent inhibitors have revealed new therapeutic targets in disease-causing parasites and have shown utility as chemoproteomic probes for interrogating kinase occupancy in living cells.
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Affiliation(s)
- Rand M Miller
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California, USA
| | - Jack Taunton
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA.
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35
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Hari SB, Perera BGK, Ranjitkar P, Seeliger MA, Maly DJ. Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src. ACS Chem Biol 2013; 8:2734-43. [PMID: 24106839 DOI: 10.1021/cb400663k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases.
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Affiliation(s)
- Sanjay B. Hari
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - B. Gayani K. Perera
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Pratistha Ranjitkar
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York 11794, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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36
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Abstract
Protein kinases represent one of the largest families of genes found in eukaryotes. Kinases mediate distinct cellular processes ranging from proliferation, differentiation, survival, and apoptosis. Ligand-mediated activation of receptor kinases can lead to the production of endogenous hydrogen peroxide (H₂O₂) by membrane-bound NADPH oxidases. In turn, H₂O₂ can be utilized as a secondary messenger in signal transduction pathways. This review presents an overview of the molecular mechanisms involved in redox regulation of protein kinases and its effects on signaling cascades. In the first half, we will focus primarily on receptor tyrosine kinases (RTKs), whereas the latter will concentrate on downstream non-receptor kinases involved in relaying stimulant response. Select examples from the literature are used to highlight the functional role of H₂O₂ regarding kinase activity, as well as the components involved in H₂O₂ production and regulation during cellular signaling. In addition, studies demonstrating direct modulation of protein kinases by H₂O₂ through cysteine oxidation will be emphasized. Identification of these redox-sensitive residues may help uncover signaling mechanisms conserved within kinase subfamilies. In some cases, these residues can even be exploited as targets for the development of new therapeutics. Continued efforts in this field will further basic understanding of kinase redox regulation, and delineate the mechanisms involved in physiological and pathological H₂O₂ responses.
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Affiliation(s)
- Thu H Truong
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
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37
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Gushwa NN, Kang S, Chen J, Taunton J. Selective targeting of distinct active site nucleophiles by irreversible SRC-family kinase inhibitors. J Am Chem Soc 2012. [PMID: 23190395 DOI: 10.1021/ja310659j] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Src-family tyrosine kinases play pivotal roles in human physiology and disease, and several drugs that target members of this family are in clinical use. None of these drugs appear to discriminate among closely related kinases. However, assessing their selectivity toward endogenous kinases in living cells remains a significant challenge. Here, we report the design of two Src-directed chemical probes, each consisting of a nucleoside scaffold with a 5'-electrophile. A 5'-fluorosulfonylbenzoate (1) reacts with the conserved catalytic lysine (Lys295) and shows little discrimination among related kinases. By contrast, a 5'-vinylsulfonate (2) reacts with a poorly conserved, proximal cysteine (Cys277) found in three Src-family and six unrelated kinases. Both 1 and 2 bear an alkyne tag and efficiently label their respective endogenous kinase targets in intact cells. Using 1 as a competitive probe, we determined the extent to which ponatinib, a clinical Bcr-Abl inhibitor, targets Src-family kinases. Remarkably, while ponatinib had little effect on endogenous Fyn or Src, it potently blocked the critical T-cell kinase, Lck. Probes 1 and 2 thus enable competitive profiling versus distinct kinase subsets in living cells.
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Affiliation(s)
- Nathan N Gushwa
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94158, United States
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