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Ying S, Chi H, Wu X, Zeng P, Chen J, Fu T, Fu W, Zhang P, Tan W. Selective and Orally Bioavailable c-Met PROTACs for the Treatment of c-Met-Addicted Cancer. J Med Chem 2024. [PMID: 39348183 DOI: 10.1021/acs.jmedchem.3c02417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
c-Met is an attractive therapeutic target in multiple tumors. Previous studies have discovered some effective proteolysis-targeting chimeras (PROTACs) able to degrade c-Met; however, the structure-activity relationship (SAR), degradation selectivity, and pharmacokinetic profiles of c-Met PROTACs have, to date, remained largely unknown. Herein, through extensive SAR studies on various warheads, linkers, and E3 ligase ligands, a novel potent c-Met PROTAC Met-DD4 was identified. Our results suggested that Met-DD4 could induce robust c-Met degradation with excellent selectivity (DC50 = 6.21 nM), substantially killing the c-Met-addicted cancer cells (IC50 = 4.37 nM). Furthermore, in vivo studies showed that Met-DD4 could achieve excellent oral bioavailability and c-Met degradation, strongly retarding tumor growth with minute organ toxicity. Overall, this study reveals that targeted degradation of c-Met is a promising strategy for the treatment of c-Met-addicted cancers and provides novel lead compounds for the clinical translation of c-Met PROTACs.
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Affiliation(s)
- Shilong Ying
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Hongli Chi
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Xiaoqiu Wu
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Pingping Zeng
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Jinling Chen
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ting Fu
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weitao Fu
- Insitute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230601, China
| | - Penghui Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Ma L, Li Y, Luo R, Wang Y, Cao J, Fu W, Qian B, Zheng L, Tang L, Lv X, Zheng L, Liang G, Chen L. Discovery of a Selective and Orally Bioavailable FGFR2 Degrader for Treating Gastric Cancer. J Med Chem 2023. [PMID: 37220310 DOI: 10.1021/acs.jmedchem.3c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Abnormal activation of fibroblast growth factor receptors (FGFRs) results in the development and progression of human cancers. FGFR2 is frequently amplified or mutated in cancers; therefore, it is an attractive target for tumor therapy. Despite the development of several pan-FGFR inhibitors, their long-term therapeutic efficacy is hindered by acquired mutations and low isoform selectivity. Herein, we report the discovery of an efficient and selective FGFR2 proteolysis-targeting chimeric molecule, LC-MB12, that incorporates an essential rigid linker. LC-MB12 preferentially internalizes and degrades membrane-bound FGFR2 among the four FGFR isoforms; this may promote greater clinical benefits. LC-MB12 exhibits superior potency in FGFR signaling suppression and anti-proliferative activity compared to the parental inhibitor. Furthermore, LC-MB12 is orally bioavailable and shows significant antitumor effects in FGFR2-dependent gastric cancer in vivo. Taken together, LC-MB12 is a candidate FGFR2 degrader for alternative FGFR2-targeting strategies and offers a promising starting point for drug development.
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Affiliation(s)
- Lin Ma
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Yingying Li
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Ruixiang Luo
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Yuhan Wang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Jiaqi Cao
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Weitao Fu
- Department of Computer-Aided Drug Design, Jiangsu Vcare PharmaTech Co. Ltd., Nanjing 211800, China
| | - Bolan Qian
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lei Zheng
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Longguang Tang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 322000, China
| | - Xinting Lv
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lulu Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang 310000, China
| | - Guang Liang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lingfeng Chen
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
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Luo R, Fu W, Shao J, Ma L, Shuai S, Xu Y, Jiang Z, Ye Z, Zheng L, Zheng L, Yu J, Zhang Y, Yin L, Tu L, Lv X, Li J, Liang G, Chen L. Discovery of a potent and selective allosteric inhibitor targeting the SHP2 tunnel site for RTK-driven cancer treatment. Eur J Med Chem 2023; 253:115305. [PMID: 37023678 DOI: 10.1016/j.ejmech.2023.115305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Src homology 2 domain-containing phosphatase 2 (SHP2) is a cytoplasmic protein tyrosine phosphatase (PTP) that regulates signal transduction of receptor tyrosine kinases (RTKs). Abnormal SHP2 activity is associated with tumorigenesis and metastasis. Because SHP2 contains multiple allosteric sites, identifying inhibitors at specific allosteric binding sites remains challenging. Here, we used structure-based virtual screening to directly search for the SHP2 "tunnel site" allosteric inhibitor. A novel hit (70) was identified as the SHP2 allosteric inhibitor with an IC50 of 10.2 μM against full-length SHP2. Derivatization of hit compound 70 using molecular modeling-guided structure-based modification allowed the discovery of an effective and selective SHP2 inhibitor, compound 129, with 122-fold improved potency compared to the hit. Further studies revealed that 129 effectively inhibited signaling in multiple RTK-driven cancers and RTK inhibitor-resistant cancer cells. Remarkably, 129 was orally bioavailable (F = 55%) and significantly inhibited tumor growth in haematological malignancy. Taken together, compound 129 developed in this study may serve as a promising lead or candidate for cancers bearing RTK oncogenic drivers and SHP2-related diseases.
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Affiliation(s)
- Ruixiang Luo
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Weitao Fu
- Department of Computer-Aided Drug Design, Jiangsu Vcare PharmaTech Co. Ltd., Nanjing, 211800, China
| | - Jingjing Shao
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Lin Ma
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Sujuan Shuai
- Department of Pharmacy, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China
| | - Ying Xu
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Zheng Jiang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Zenghui Ye
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Lulu Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, 310000, China
| | - Lei Zheng
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Jie Yu
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Yawen Zhang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Lina Yin
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Linglan Tu
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Xinting Lv
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China
| | - Jie Li
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China; Department of Pharmacy, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
| | - Guang Liang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Lingfeng Chen
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310012, China.
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Sun HH, Wang ZZ, Gao YY, Hao GF, Yang GF. Protein Kinases as Potential Targets Contribute to the Development of Agrochemicals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:52-64. [PMID: 36592042 DOI: 10.1021/acs.jafc.2c06222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Using agrochemicals against pest insects, fungi, and weeds plays a major part in maintaining and improving crop yields, which helps to solve the issue of food security. Due to the limited targets and resistance of agrochemicals, protein kinases are regarded as attractive potential targets to develop new agrochemicals. Recently, a lot of investigations have shown the extension of agrochemicals by targeting protein kinases, implying an increasing concern for this kind of method. However, few people have summarized and discussed the targetability of protein kinases contributing to the development of agrochemicals. In this work, we introduce the research on protein kinases as potential targets used in crop protection and discuss the prospects of protein kinases in the field of agrochemical development. This study may not only provide guidance for the contribution of protein kinases to the development of agrochemicals but also help nonprofessionals such as students learn and understand the role of protein kinases quickly.
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Affiliation(s)
- Hao-Han Sun
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Zhi-Zheng Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yang-Yang Gao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, People's Republic of China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
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5
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Yang L, Yang G, Bing Z, Tian Y, Niu Y, Huang L, Yang L. Transformer-Based Generative Model Accelerating the Development of Novel BRAF Inhibitors. ACS OMEGA 2021; 6:33864-33873. [PMID: 34926933 PMCID: PMC8674994 DOI: 10.1021/acsomega.1c05145] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
The de novo drug design based on SMILES format is a typical sequence-processing problem. Previous methods based on recurrent neural network (RNN) exhibit limitation in capturing long-range dependency, resulting in a high invalid percentage in generated molecules. Recent studies have shown the potential of Transformer architecture to increase the capacity of handling sequence data. In this work, the encoder module in the Transformer is used to build a generative model. First, we train a Transformer-encoder-based generative model to learn the grammatical rules of known drug molecules and a predictive model to predict the activity of the molecules. Subsequently, transfer learning and reinforcement learning were used to fine-tune and optimize the generative model, respectively, to design new molecules with desirable activity. Compared with previous RNN-based methods, our method has improved the percentage of generating chemically valid molecules (from 95.6 to 98.2%), the structural diversity of the generated molecules, and the feasibility of molecular synthesis. The pipeline is validated by designing inhibitors against the human BRAF protein. Molecular docking and binding mode analysis showed that our method can generate small molecules with higher activity than those carrying ligands in the crystal structure and have similar interaction sites with these ligands, which can provide new ideas and suggestions for pharmaceutical chemists.
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Affiliation(s)
- Lijuan Yang
- Institute
of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- School
of Physics and Technology, Lanzhou University, Lanzhou 730000, China
- School
of Physics, University of Chinese Academy
of Sciences, Beijing 100049, China
- Advanced
Energy Science and Technology, Guangdong
Laboratory, Huizhou 516000, China
| | - Guanghui Yang
- Institute
of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Advanced
Energy Science and Technology, Guangdong
Laboratory, Huizhou 516000, China
| | - Zhitong Bing
- Institute
of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Advanced
Energy Science and Technology, Guangdong
Laboratory, Huizhou 516000, China
| | - Yuan Tian
- Institute
of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- School
of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Yuzhen Niu
- Shandong
Provincial Research Center for Bioinformatic Engineering and Technique,
School of Life Sciences, Shandong University
of Technology, Zibo 255000, China
| | - Liang Huang
- School
of Physics and Technology, Lanzhou University, Lanzhou 730000, China
| | - Lei Yang
- Institute
of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Advanced
Energy Science and Technology, Guangdong
Laboratory, Huizhou 516000, China
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