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Guo Z, Duan Y, Sun K, Zheng T, Liu J, Xu S, Xu J. Advances in SHP2 tunnel allosteric inhibitors and bifunctional molecules. Eur J Med Chem 2024; 275:116579. [PMID: 38889611 DOI: 10.1016/j.ejmech.2024.116579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
SHP2 is a non-receptor tyrosine phosphatase encoded by PTPN11, which performs the functions of regulating cell proliferation, differentiation, apoptosis, and survival through removing tyrosine phosphorylation and modulating various signaling pathways. The overexpression of SHP2 or its mutations is related to developmental diseases and several cancers. Numerous allosteric inhibitors with striking inhibitory potency against SHP2 allosteric pockets have recently been identified, and several SHP2 tunnel allosteric inhibitors have been applied in clinical trials to treat cancers. However, based on clinical results, the efficacy of single-agent treatments has been proven to be suboptimal. Most clinical trials involving SHP2 inhibitors have adopted drug combination strategies. This review briefly discusses the research progress on SHP2 allosteric inhibitors and pathway-dependent drug combination strategies for SHP2 in cancer therapy. In addition, we summarize the current bifunctional molecules of SHP2 and elaborate on the design and structural optimization strategies of these bifunctional molecules in detail, offering further direction for the research on novel SHP2 inhibitors.
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Affiliation(s)
- Zhichao Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Yiping Duan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Kai Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Tiandong Zheng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Jie Liu
- Department of Organic Chemistry, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
| | - Shengtao Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
| | - Jinyi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
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Hu F, Chang F, Tao L, Sun X, Liu L, Zhao Y, Han Z, Li C. Prediction of Protein Allosteric Sites with Transfer Entropy and Spatial Neighbor-Based Evolutionary Information Learned by an Ensemble Model. J Chem Inf Model 2024; 64:6197-6204. [PMID: 39075972 DOI: 10.1021/acs.jcim.4c00544] [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: 07/31/2024]
Abstract
Allostery is one of the most direct and efficient ways to regulate protein functions. The diverse allosteric sites make it possible to design allosteric modulators of differential selectivity and improved safety compared with those of orthosteric drugs targeting conserved orthosteric sites. Here, we develop an ensemble machine learning method AllosES to predict protein allosteric sites in which the new and effective features are utilized, including the entropy transfer-based dynamic property, secondary structure features, and our previously proposed spatial neighbor-based evolutionary information besides the traditional physicochemical properties. To overcome the class imbalance problem, the multiple grouping strategy is proposed, which is applied to feature selection and model construction. The ensemble model is constructed where multiple submodels are trained on multiple training subsets, respectively, and their results are then integrated to be the final output. AllosES achieves a prediction performance of 0.556 MCC on the independent test set D24, and additionally, AllosES can rank the real allosteric sites in the top three for 83.3/89.3% of allosteric proteins from the test set D24/D28, outperforming the state-of-the-art peer methods. The comprehensive results demonstrate that AllosES is a promising method for protein allosteric site prediction. The source code is available at https://github.com/ChunhuaLab/AllosES.
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Affiliation(s)
- Fangrui Hu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Fubin Chang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Lianci Tao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaohan Sun
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Lamei Liu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Yingchun Zhao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Zhongjie Han
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
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Adhikari N, Ayyannan SR. Development and validation of machine learning models for the prediction of SH-2 containing protein tyrosine phosphatase 2 inhibitors. Mol Divers 2024; 28:1889-1905. [PMID: 37552436 DOI: 10.1007/s11030-023-10710-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
Discovery and development of a new drug to the market is a highly challenging and resource consuming process. Although, modern drug discovery technologies have enabled the rapid identification of lead compounds, translation of the lead compounds into successful clinical candidates remains a big challenge. In recent years, the availability of massive structural and biological data of diverse small molecules and macromolecules has helped the researchers to deep mine the multidimensional data with the help of artificial intelligence-based predictive tools to draw useful insights on the structural features of biological or therapeutic significance. The aim of this study was to utilize the available data on small molecule (SH2)-containing protein tyrosine phosphatase 2 (SHP2) inhibitors to build and develop machine learning (ML) models that can predict the SHP2 inhibitory potential of new compounds. The dataset contained 2739 unique small molecule SHP2 inhibitors obtained from the BindingDB, ChEMBL and recent literature. After curation of the data, the predictive models such as XGBoost, K nearest neighbours, neural networks were developed and validated through a tenfold cross-validation testing procedure. Out of the seven models developed, the XGBoost model showed an excellent performance with ROC AUC score of 0.96 and accuracy of 0.97 on the test data. Moreover, the Shapley Additive Explanations method was applied to assess a more in-depth understanding of the influence of variables on the model's predictions. In summary, the XGBoost model developed in this study can be useful in the identification of novel SHP2 inhibitors and therefore, can accelerate the discovery of novel therapeutics for cancer therapy.
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Affiliation(s)
- Nilanjan Adhikari
- Pharmaceutical Chemistry Research Laboratory II, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, UP, 221005, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory II, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, UP, 221005, India.
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Tang K, Wang S, Feng S, Yang X, Guo Y, Ren X, Bai L, Yu B, Liu HM, Song Y. Discovery of TK-642 as a highly potent, selective, orally bioavailable pyrazolopyrazine-based allosteric SHP2 inhibitor. Acta Pharm Sin B 2024; 14:3624-3642. [PMID: 39234614 PMCID: PMC11372460 DOI: 10.1016/j.apsb.2024.03.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/20/2024] [Accepted: 03/14/2024] [Indexed: 09/06/2024] Open
Abstract
Src homology-2-containing protein tyrosine phosphatase 2 (SHP2) is a promising therapeutic target for cancer therapy. In this work, we presented the structure-guided design of 5,6-fused bicyclic allosteric SHP2 inhibitors, leading to the identification of pyrazolopyrazine-based TK-642 as a highly potent, selective, orally bioavailable allosteric SHP2 inhibitor (SHP2WT IC50 = 2.7 nmol/L) with favorable pharmacokinetic profiles (F = 42.5%; t 1/2 = 2.47 h). Both dual inhibition biochemical assay and docking analysis indicated that TK-642 likely bound to the "tunnel" allosteric site of SHP2. TK-642 could effectively suppress cell proliferation (KYSE-520 cells IC50 = 5.73 μmol/L) and induce apoptosis in esophageal cancer cells by targeting the SHP2-mediated AKT and ERK signaling pathways. Additionally, oral administration of TK-642 also demonstrated effective anti-tumor effects in the KYSE-520 xenograft mouse model, with a T/C value of 83.69%. Collectively, TK-642 may warrant further investigation as a promising lead compound for the treatment of esophageal cancer.
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Affiliation(s)
- Kai Tang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Shu Wang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Siqi Feng
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Xinyu Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Yueyang Guo
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Xiangli Ren
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Linyue Bai
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- College of Chemistry, Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Zhengzhou University, Zhengzhou 450001, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450000, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
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Zhu C, Zhao H, Yang W, Chen K, Liu X, Yu Y, Li R, Tan R, Yu Z. Design, Synthesis and Antitumor Activity of a Novel Class of SHP2 Allosteric Inhibitors with a Furanyl Amide-Based Scaffold. J Med Chem 2024. [PMID: 39066713 DOI: 10.1021/acs.jmedchem.4c01217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
SHP2 plays a critical role in modulating tumor growth and PD-1-related signaling pathway, thereby serving as an attractive antitumor target. To date, no antitumor drugs targeting SHP2 have been approved, and hence, the search of SHP2 inhibitors with new chemical scaffolds is urgently needed. Herein, we developed a novel SHP2 allosteric inhibitor SDUY038 with a furanyl amide scaffold, demonstrating potent binding affinity (KD = 0.29 μM), enzymatic activity (IC50 = 1.2 μM) and similar binding interactions to SHP099. At the cellular level, SDUY038 exhibited pan-antitumor activity (IC50 = 7-24 μM) by suppressing pERK expression. Furthermore, SDUY038 significantly inhibited tumor growth in both xenograft and organoid models. Additionally, SDUY038 displayed acceptable bioavailability (F = 14%) and half-life time (t1/2 = 3.95 h). Conclusively, this study introduces the furanyl amide scaffold as a novel class of SHP2 allosteric inhibitors, offering promising lead compounds for further development of new antitumor therapies targeting SHP2.
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Affiliation(s)
- Chengchun Zhu
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P.R. China
| | - Haiyang Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, No. 59, Middle Section of Qinglong Avenue, Mianyang 621010, P.R. China
- Center for Organoids and Translational Pharmacology, Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Institute for Translational Chinese Medicine, Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, P.R. China
| | - Wenting Yang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P.R. China
| | - Kai Chen
- Center for New Drug Evaluation, Shandong Academy of Pharmaceutical Sciences, Jinan 250000, P.R. China
| | - Xiaoyu Liu
- Center for New Drug Evaluation, Shandong Academy of Pharmaceutical Sciences, Jinan 250000, P.R. China
| | - Yan Yu
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P.R. China
| | - Rui Li
- Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Chengdu 610041, P.R. China
| | - Ruirong Tan
- Center for Organoids and Translational Pharmacology, Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Institute for Translational Chinese Medicine, Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, P.R. China
| | - Zhiyi Yu
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P.R. China
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6
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Liu YY, Yi YJ, Ye J, Hu AX. Design, synthesis and neuraminidase inhibitory activity of 4-methyl-5-(3-phenylacryloyl) thiazoles. Mol Divers 2024; 28:1129-1140. [PMID: 36959424 DOI: 10.1007/s11030-023-10639-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/17/2023] [Indexed: 03/25/2023]
Abstract
A series of 4-methyl-5-(3-phenylacryloyl)thiazoles based on chalcones were designed, synthesized and evaluated for their influenza neuraminidase (NA) inhibitory activity in vitro. A preliminary structure-activity relationship (SAR) analysis showed that thiazoles bearing amide had greater potency. It also showed that mono-hydroxyl group at 4-position on phenyl ring was more effective than other electron-releasing groups or electron-withdraw groups. Compounds A2 and A26 were more potent against NA with IC50 values of 8.2 ± 0.5 μg/mL and 6.2 ± 1.4 μg/mL, respectively. Molecular docking study demonstrated that thiazoles skeleton was benefit for the NA inhibitory activity.
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Affiliation(s)
- Yu-Yang Liu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yang-Jie Yi
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jiao Ye
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Ai-Xi Hu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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Yang L, Zhao H, Yuan F, Chen M, Ma N, Yin Z, Liu H, Guo Y. Computational study on the binding mechanism of allosteric drug TNO155 inhibiting SHP2 E76A. Mol Divers 2024:10.1007/s11030-024-10881-1. [PMID: 38807000 DOI: 10.1007/s11030-024-10881-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
E76A mutations of SHP2 have been reported to associate with genetic developmental diseases and cancers, and TNO155 is one of the effective inhibitors targeted to the allosteric site 1, which has already entered the clinical stage. However, the detailed binding mechanism between them still needs further clarification at micro-atomic level. In this study, the binding mechanism of TNO155 inhibiting SHP2E76A and the superiorities of TNO155 at binding affinity and dynamic interactive behavior with SHP2E76A were probed utilizing a series of computational drug design technologies. The results show that SHP2E76A forms tighter interaction with TNO155 compared to SHP099. SHP2E76A-TNO155 exhibits the largest electrostatic interaction among all complex systems, which can be manifested by the strong hydrogen bond interactions formed by two electrically charged residues, Arg111 and Glu250. Notably, in SHP2E76A-TNO155 system, Asp489 makes an additional substantial beneficial contribution. The E76A mutation brings stronger residue positive correlation and a larger conformation fluctuation between N-CH2 and PTP domains, resulting in tighter binding between TNO155 and SHP2E76A. This study offers valuable insights for the further design and development of novel SHP2E76A allosteric inhibitors.
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Affiliation(s)
- Longhua Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Huijian Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fanru Yuan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Mengguo Chen
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Nannan Ma
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhili Yin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Henan Province for Drug Quality and Evaluation, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, 450001, China
| | - Yong Guo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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Wang P, Han Y, Pan W, Du J, Zuo D, Ba Y, Zhang H. Tyrosine phosphatase SHP2 aggravates tumor progression and glycolysis by dephosphorylating PKM2 in gastric cancer. MedComm (Beijing) 2024; 5:e527. [PMID: 38576457 PMCID: PMC10993348 DOI: 10.1002/mco2.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 11/26/2023] [Accepted: 12/22/2023] [Indexed: 04/06/2024] Open
Abstract
Gastric cancer (GC) is among the most lethal human malignancies, yet it remains hampered by challenges in fronter of molecular-guided targeted therapy to direct clinical treatment strategies. The protein tyrosine phosphatase Src homology 2 domain-containing phosphatase 2 (SHP2) is involved in the malignant progression of GC. However, the detailed mechanisms of the posttranslational modifications of SHP2 remain poorly understood. Herein, we demonstrated that an allosteric SHP2 inhibitor, SHP099, was able to block tumor proliferation and migration of GC by dephosphorylating the pyruvate kinase M2 type (PKM2) protein. Mechanistically, we found that PKM2 is a bona fide target of SHP2. The dephosphorylation and activation of PKM2 by SHP2 are necessary to exacerbate tumor progression and GC glycolysis. Moreover, we demonstrated a strong correlation between the phosphorylation level of PKM2 and adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) in GC cells. Notably, the low phosphorylation expression of AMPK was negatively correlated with activated SHP2. Besides, we proved that cisplatin could activate SHP2 and SHP099 increased sensitivity to cisplatin in GC. Taken together, our results provide evidence that the SHP2/PKM2/AMPK axis exerts a key role in GC progression and glycolysis and could be a viable therapeutic approach for the therapy of GC.
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Affiliation(s)
- Peiyun Wang
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Yueting Han
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Wen Pan
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Jian Du
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Duo Zuo
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Yi Ba
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Haiyang Zhang
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
- The Institute of Translational MedicineTianjin Union Medical Center of Nankai UniversityTianjinChina
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Bhavana, Kohal R, Kumari P, Das Gupta G, Kumar Verma S. Druggable targets of protein tyrosine phosphatase Family, viz. PTP1B, SHP2, Cdc25, and LMW-PTP: Current scenario on medicinal Attributes, and SAR insights. Bioorg Chem 2024; 144:107121. [PMID: 38237392 DOI: 10.1016/j.bioorg.2024.107121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/02/2024] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Protein tyrosine phosphatases (PTPs) are the class of dephosphorylation enzymes that catalyze the removal of phosphate groups from tyrosine residues on proteins responsible for various cellular processes. Any disbalance in signal pathways mediated by PTPs leads to various disease conditions like diabetes, obesity, cancers, and autoimmune disorders. Amongst the PTP superfamily, PTP1B, SHP2, Cdc25, and LMW-PTP have been prioritized as druggable targets for developing medicinal agents. PTP1B is an intracellular PTP enzyme that downregulates insulin and leptin signaling pathways and is involved in insulin resistance and glucose homeostasis. SHP2 is involved in the RAS-MAPK pathway and T cell immunity. Cdk-cyclin complex activation occurs by Cdc25-PTPs involved in cell cycle regulation. LMW-PTPs are involved in PDGF/PDGFR, Eph/ephrin, and insulin signaling pathways, resulting in certain diseases like diabetes mellitus, obesity, and cancer. The signaling cascades of PTP1B, SHP2, Cdc25, and LMW-PTPs have been described to rationalize their medicinal importance in the pathophysiology of diabetes, obesity, and cancer. Their binding sites have been explored to overcome the hurdles in discovering target selective molecules with optimum potency. Recent developments in the synthetic molecules bearing heterocyclic moieties against these targets have been explored to gain insight into structural features. The elaborated SAR investigation revealed the effect of substituents on the potency and target selectivity, which can be implicated in the further discovery of newer medicinal agents targeting the druggable members of the PTP superfamily.
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Affiliation(s)
- Bhavana
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Rupali Kohal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Preety Kumari
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Ghanshyam Das Gupta
- Department of Pharmaceutics, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India.
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Pinto AF, Nunes JS, Severino Martins JE, Leal AC, Silva CCVC, da Silva AJFS, da Cruz Olímpio DS, da Silva ETN, Campos TA, Lima Leite AC. Thiazole, Isatin and Phthalimide Derivatives Tested in vivo against Cancer Models: A Literature Review of the Last Six Years. Curr Med Chem 2024; 31:2991-3032. [PMID: 37170994 DOI: 10.2174/0929867330666230426154055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Cancer is a disease characterized by the abnormal multiplication of cells and is the second leading cause of death in the world. The search for new effective and safe anticancer compounds is ongoing due to factors such as low selectivity, high toxicity, and multidrug resistance. Thus, heterocyclic compounds derived from isatin, thiazole and phthalimide that have achieved promising in vitro anticancer activity have been tested in vivo and in clinical trials. OBJECTIVE This review focused on the compilation of promising data from thiazole, isatin, and phthalimide derivatives, reported in the literature between 2015 and 2022, with in vivo anticancer activity and clinical trials. METHODS A bibliographic search was carried out in the PUBMED, MEDLINE, ELSEVIER, and CAPES PERIODIC databases, selecting relevant works for each pharmacophoric group with in vivo antitumor activity in the last 6 years. RESULTS In our study, 68 articles that fit the scope were selected and critically analyzed. These articles were organized considering the type of antitumor activity and their year of publication. Some compounds reported here demonstrated potent antitumor activity against several tumor types. CONCLUSION This review allowed us to highlight works that reported promising structures for the treatment of various cancer types and also demonstrated that the privileged structures thiazole, isatin and phthalimide are important in the design of new syntheses and molecular optimization of compounds with antitumor activity.
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Affiliation(s)
- Aline Ferreira Pinto
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
| | - Janine Siqueira Nunes
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
| | - José Eduardo Severino Martins
- Regulatory Affairs Advisory, Empresa Brasileira de Hemoderivados e Biotecnologia (HEMOBRAS), CEP 51021-410, Recife, PE, Brazil
| | - Amanda Calazans Leal
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
| | - Carla Cauanny Vieira Costa Silva
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
| | - Anderson José Firmino Santos da Silva
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
| | - Daiane Santiago da Cruz Olímpio
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
| | - Elineide Tayse Noberto da Silva
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
| | - Thiers Araújo Campos
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
| | - Ana Cristina Lima Leite
- Laboratory of Planning in Medicinal Chemistry, Department of Pharmaceutical Sciences, Center for Health Sciences, Federal University of Pernambuco, 50740-520, Recife, PE, Brazil
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Segura J, Rose Y, Bi C, Duarte J, Burley SK, Bittrich S. RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins. FRONTIERS IN BIOINFORMATICS 2023; 3:1311287. [PMID: 38111685 PMCID: PMC10726007 DOI: 10.3389/fbinf.2023.1311287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023] Open
Abstract
Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.
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Affiliation(s)
- Joan Segura
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, CA, United States
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, CA, United States
| | - Chunxiao Bi
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, CA, United States
| | - Jose Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, CA, United States
| | - Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, CA, United States
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Sebastian Bittrich
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, CA, United States
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12
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Wang N, Zhu S, Lv D, Wang Y, Khawar MB, Sun H. Allosteric modulation of SHP2: Quest from known to unknown. Drug Dev Res 2023; 84:1395-1410. [PMID: 37583266 DOI: 10.1002/ddr.22100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/17/2023]
Abstract
Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) is a key regulatory factor in the cell cycle and its activating mutations play an important role in the development of various cancers, making it an important target for antitumor drugs. Due to the highly conserved amino acid sequence and positively charged nature of the active site of SHP2, it is difficult to discover inhibitors with high affinity for the catalytic site of SHP2 and sufficient cell permeability, making it considered an "undruggable" target. However, the discovery of allosteric regulation mechanisms provides new opportunities for transforming undruggable targets into druggable ones. Given the limitations of orthosteric inhibitors, SHP2 allosteric inhibitors have become a more selective and safer research direction. In this review, we elucidate the oncogenic mechanism of SHP2 and summarize the discovery methods of SHP2 allosteric inhibitors, providing new strategies for the design and improvement of SHP2 allosteric inhibitors.
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Affiliation(s)
- Ning Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
| | - Shilin Zhu
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Dan Lv
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
- School of Life Sciences, Anqing Normal University, Anqing, China
| | - Yajun Wang
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Muhammad B Khawar
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Haibo Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
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13
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Liao J, Yang J, Li X, Hu C, Zhu W, Zhou Y, Zou Y, Guo M, Chen Z, Li X, Dai J, Xu Y, Zheng Z, Chen P, Cho WJ, Liang G, Tang Q. Discovery of the Diphenyl 6-Oxo-1,6-dihydropyridazine-3-carboxylate/carboxamide Analogue J27 for the Treatment of Acute Lung Injury and Sepsis by Targeting JNK2 and Inhibiting the JNK2-NF-κB/MAPK Pathway. J Med Chem 2023; 66:12304-12323. [PMID: 37643372 DOI: 10.1021/acs.jmedchem.3c00832] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Acute lung injury (ALI) and sepsis are both serious and complex conditions associated with high mortality, yet there are no effective treatments. Herein, we designed and synthesized a series of diphenyl 6-oxo-1,6-dihydropyridazine-3-carboxylate/carboxamide analogues exhibiting anti-inflammatory activity. The optimal compound J27 decreased the release of TNF-α and IL-6 in mouse and human cells J774A.1 and THP-1 (IL-6 IC50 = 0.22 μM) through the NF-κB/MAPK pathway. J27 demonstrated remarkable protection against ALI and sepsis in vivo and exhibited good safety in subacute toxicity experiments. Pharmacokinetic study indicated that J27 had good bioavailability (30.74%). To our surprise, J27 could target JNK2 with a totally new molecular skeleton compared with the only few JNK2 inhibitors reported. Moreover, there is no report that JNK2 inhibitors could apply for ALI and sepsis. Therefore, this work provides a new lead structure for the study of JNK2 inhibitors and a new target of JNK2 to treat ALI and sepsis.
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Affiliation(s)
- Jing Liao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- School of Pharmacy, Hangzhou Medical College, Hangzhou 311399, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Jun Yang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiaobo Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Chenghong Hu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Weiwei Zhu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Ying Zhou
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yu Zou
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Mi Guo
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Zhichao Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiang Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Jintian Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Yuye Xu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Zhiwei Zheng
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- College of Pharmacy, Chonnam National University, Gwangju 61186, Korea
| | - Pan Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- College of Pharmacy, Chonnam National University, Gwangju 61186, Korea
| | - Won-Jea Cho
- College of Pharmacy, Chonnam National University, Gwangju 61186, Korea
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- School of Pharmacy, Hangzhou Medical College, Hangzhou 311399, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
| | - Qidong Tang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325024, China
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14
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Liu Y, Xie B, Chen Q. RAS signaling and immune cells: a sinister crosstalk in the tumor microenvironment. J Transl Med 2023; 21:595. [PMID: 37670322 PMCID: PMC10481548 DOI: 10.1186/s12967-023-04486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/30/2023] [Indexed: 09/07/2023] Open
Abstract
The rat sarcoma virus (RAS) gene is the most commonly mutated oncogene in cancer, with about 19% of cancer patients carrying RAS mutations. Studies on the interaction between RAS mutation and tumor immune microenvironment (TIM) have been flourishing in recent years. More and more evidence has proved that RAS signals regulate immune cells' recruitment, activation, and differentiation while assisting tumor cells to evade immune surveillance. This review concluded the direct and indirect treatment strategies for RAS mutations. In addition, we updated the underlying mechanisms by which RAS signaling modulated immune infiltration and immune escape. Finally, we discussed advances in RAS-targeted immunotherapies, including cancer vaccines and adoptive cell therapies, with a particular focus on combination strategies with personalized therapy and great potential to achieve lasting clinical benefits.
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Affiliation(s)
- Yongting Liu
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Bin Xie
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qiong Chen
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, China.
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15
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Welsh CL, Allen S, Madan LK. Setting sail: Maneuvering SHP2 activity and its effects in cancer. Adv Cancer Res 2023; 160:17-60. [PMID: 37704288 PMCID: PMC10500121 DOI: 10.1016/bs.acr.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Since the discovery of tyrosine phosphorylation being a critical modulator of cancer signaling, proteins regulating phosphotyrosine levels in cells have fast become targets of therapeutic intervention. The nonreceptor protein tyrosine phosphatase (PTP) coded by the PTPN11 gene "SHP2" integrates phosphotyrosine signaling from growth factor receptors into the RAS/RAF/ERK pathway and is centrally positioned in processes regulating cell development and oncogenic transformation. Dysregulation of SHP2 expression or activity is linked to tumorigenesis and developmental defects. Even as a compelling anti-cancer target, SHP2 was considered "undruggable" for a long time owing to its conserved catalytic PTP domain that evaded drug development. Recently, SHP2 has risen from the "undruggable curse" with the discovery of small molecules that manipulate its intrinsic allostery for effective inhibition. SHP2's unique domain arrangement and conformation(s) allow for a truly novel paradigm of inhibitor development relying on skillful targeting of noncatalytic sites on proteins. In this review we summarize the biological functions, signaling properties, structural attributes, allostery and inhibitors of SHP2.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Sarah Allen
- Department of Pediatrics, Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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16
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Jensen NR, Kelly RR, Kelly KD, Khoo SK, Sidles SJ, LaRue AC. From Stem to Sternum: The Role of Shp2 in the Skeleton. Calcif Tissue Int 2023; 112:403-421. [PMID: 36422682 DOI: 10.1007/s00223-022-01042-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/05/2022] [Indexed: 11/25/2022]
Abstract
Src homology-2 domain-containing phosphatase 2 (SHP2) is a ubiquitously expressed phosphatase that is vital for skeletal development and maintenance of chondrocytes, osteoblasts, and osteoclasts. Study of SHP2 function in small animal models has led to insights in phenotypes observed in SHP2-mutant human disease, such as Noonan syndrome. In recent years, allosteric SHP2 inhibitors have been developed to specifically target the protein in neoplastic processes. These inhibitors are highly specific and have great potential for disease modulation in cancer and other pathologies, including bone disorders. In this review, we discuss the importance of SHP2 and related signaling pathways (e.g., Ras/MEK/ERK, JAK/STAT, PI3K/Akt) in skeletal development. We review rodent models of pathologic processes caused by germline mutations that activate SHP2 enzymatic activity, with a focus on the skeletal phenotype seen in these patients. Finally, we discuss SHP2 inhibitors in development and their potential for disease modulation in these genetic diseases, particularly as it relates to the skeleton.
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Affiliation(s)
- Nathaniel R Jensen
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan R Kelly
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Kirsten D Kelly
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA
| | - Stephanie K Khoo
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA
| | - Sara J Sidles
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Amanda C LaRue
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA.
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA.
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17
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Stampolaki M, Malwal SR, Alvarez-Cabrera N, Gao Z, Moniruzzaman M, Babii SO, Naziris N, Rey-Cibati A, Valladares-Delgado M, Turcu AL, Baek KH, Phan TN, Lee H, Alcaraz M, Watson S, van der Watt M, Coertzen D, Efstathiou N, Chountoulesi M, Shoen CM, Papanastasiou IP, Brea J, Cynamon MH, Birkholtz LM, Kremer L, No JH, Vázquez S, Benaim G, Demetzos C, Zgurskaya HI, Dick T, Oldfield E, D. Kolocouris A. Synthesis and Testing of Analogs of the Tuberculosis Drug Candidate SQ109 against Bacteria and Protozoa: Identification of Lead Compounds against Mycobacterium abscessus and Malaria Parasites. ACS Infect Dis 2023; 9:342-364. [PMID: 36706233 PMCID: PMC10615177 DOI: 10.1021/acsinfecdis.2c00537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
SQ109 is a tuberculosis drug candidate that has high potency against Mycobacterium tuberculosis and is thought to function at least in part by blocking cell wall biosynthesis by inhibiting the MmpL3 transporter. It also has activity against bacteria and protozoan parasites that lack MmpL3, where it can act as an uncoupler, targeting lipid membranes and Ca2+ homeostasis. Here, we synthesized 18 analogs of SQ109 and tested them against M. smegmatis, M. tuberculosis, M. abscessus, Bacillus subtilis, and Escherichia coli, as well as against the protozoan parasites Trypanosoma brucei, T. cruzi, Leishmania donovani, L. mexicana, and Plasmodium falciparum. Activity against the mycobacteria was generally less than with SQ109 and was reduced by increasing the size of the alkyl adduct, but two analogs were ∼4-8-fold more active than SQ109 against M. abscessus, including a highly drug-resistant strain harboring an A309P mutation in MmpL3. There was also better activity than found with SQ109 with other bacteria and protozoa. Of particular interest, we found that the adamantyl C-2 ethyl, butyl, phenyl, and benzyl analogs had 4-10× increased activity against P. falciparum asexual blood stages, together with low toxicity to a human HepG2 cell line, making them of interest as new antimalarial drug leads. We also used surface plasmon resonance to investigate the binding of inhibitors to MmpL3 and differential scanning calorimetry to investigate binding to lipid membranes. There was no correlation between MmpL3 binding and M. tuberculosis or M. smegmatis cell activity, suggesting that MmpL3 is not a major target in mycobacteria. However, some of the more active species decreased lipid phase transition temperatures, indicating increased accumulation in membranes, which is expected to lead to enhanced uncoupler activity.
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Affiliation(s)
- Marianna Stampolaki
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Satish R. Malwal
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, USA
| | | | - Zijun Gao
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, USA
| | - Mohammad Moniruzzaman
- University of Oklahoma, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Norman, OK 73019-5251, USA
| | - Svitlana O. Babii
- University of Oklahoma, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Norman, OK 73019-5251, USA
| | - Nikolaos Naziris
- Section of Pharmaceutical Technology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - André Rey-Cibati
- Instituto de Estudios Avanzados, Caracas, Venezuela Instituto de Biología Experimental, Facultad de Ciencias, Universidad Central de Venezuela (UCV), Caracas, Venezuela
| | - Mariana Valladares-Delgado
- Instituto de Estudios Avanzados, Caracas, Venezuela Instituto de Biología Experimental, Facultad de Ciencias, Universidad Central de Venezuela (UCV), Caracas, Venezuela
| | - Andreea L. Turcu
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l’Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona, E-08028, Spain
| | - Kyung-Hwa Baek
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam-si, Republic of Korea
| | - Trong-Nhat Phan
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam-si, Republic of Korea
| | - Hyeryon Lee
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam-si, Republic of Korea
| | - Mattheo Alcaraz
- Institut de Recherche en Infectiologie de Montpellier, CNRS UMR9004, Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Savannah Watson
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
| | - Mariette van der Watt
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
| | - Dina Coertzen
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
| | - Natasa Efstathiou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Maria Chountoulesi
- Section of Pharmaceutical Technology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Carolyn M. Shoen
- Central New York Research Corporation, Veterans Affairs Medical Center, Syracuse, NY 13210, U
| | - Ioannis P. Papanastasiou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Jose Brea
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center, Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Michael H. Cynamon
- Central New York Research Corporation, Veterans Affairs Medical Center, Syracuse, NY 13210, U
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier, CNRS UMR9004, Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
- INSERM, IRIM, Montpellier, France
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam-si, Republic of Korea
| | - Santiago Vázquez
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l’Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona, E-08028, Spain
| | - Gustavo Benaim
- Instituto de Estudios Avanzados, Caracas, Venezuela Instituto de Biología Experimental, Facultad de Ciencias, Universidad Central de Venezuela (UCV), Caracas, Venezuela
| | - Costas Demetzos
- Section of Pharmaceutical Technology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Helen I. Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Norman, OK 73019-5251, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC 20007, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, USA
| | - Antonios D. Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
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18
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SH2 Domains: Folding, Binding and Therapeutical Approaches. Int J Mol Sci 2022; 23:ijms232415944. [PMID: 36555586 PMCID: PMC9783222 DOI: 10.3390/ijms232415944] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
SH2 (Src Homology 2) domains are among the best characterized and most studied protein-protein interaction (PPIs) modules able to bind and recognize sequences presenting a phosphorylated tyrosine. This post-translational modification is a key regulator of a plethora of physiological and molecular pathways in the eukaryotic cell, so SH2 domains possess a fundamental role in cell signaling. Consequently, several pathologies arise from the dysregulation of such SH2-domains mediated PPIs. In this review, we recapitulate the current knowledge about the structural, folding stability, and binding properties of SH2 domains and their roles in molecular pathways and pathogenesis. Moreover, we focus attention on the different strategies employed to modulate/inhibit SH2 domains binding. Altogether, the information gathered points to evidence that pharmacological interest in SH2 domains is highly strategic to developing new therapeutics. Moreover, a deeper understanding of the molecular determinants of the thermodynamic stability as well as of the binding properties of SH2 domains appears to be fundamental in order to improve the possibility of preventing their dysregulated interactions.
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19
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Ostapiuk YV, Barabash OV, Ostapiuk MY, Goreshnik E, Obushak MD, Schmidt A. Thiocyanatoarylation of Methyl Vinyl Ketone under Meerwein Conditions for the Synthesis of 2-Aminothiazole-Based Heterocyclic Systems. Org Lett 2022; 24:4575-4579. [PMID: 35735270 DOI: 10.1021/acs.orglett.2c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
4-Aryl-3-thiocyanatobutan-2-ones were prepared by Meerwein reactions from methyl vinyl ketone and aryldiazonium salts under copper(II) catalysis in 35-75% yields. α-Thiocyanato ketones regioselectively react with 1-methyl-3-aminopyrazole forming N-(3-pyrazolyl)-substituted 2-aminothiazoles in 80-91% yields. An ester group in position 3 of the pyrazole induced a regioselective ring-closure reaction followed by an intramolecular cyclization, which gave first representatives of a new heterocyclic system, pyrazolo[4,3-e]thiazolo[3,2-a]pyrimidine, in 74-93% yields. In addition, the preparations of 5-benzyl-4-methylthiazol-2-ones in 84-93% yields are described.
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Affiliation(s)
- Yurii V Ostapiuk
- Department of Organic Chemistry, Ivan Franko National University of Lviv, Kyryla i Mefodiya Str. 6, 79005 Lviv, Ukraine
| | - Oksana V Barabash
- Department of Organic Chemistry, Ivan Franko National University of Lviv, Kyryla i Mefodiya Str. 6, 79005 Lviv, Ukraine
| | - Mary Y Ostapiuk
- Department of Organic Chemistry, Ivan Franko National University of Lviv, Kyryla i Mefodiya Str. 6, 79005 Lviv, Ukraine
| | - Evgeny Goreshnik
- Department of Inorganic Chemistry and Technology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Mykola D Obushak
- Department of Organic Chemistry, Ivan Franko National University of Lviv, Kyryla i Mefodiya Str. 6, 79005 Lviv, Ukraine
| | - Andreas Schmidt
- Institute of Organic Chemistry, Clausthal University of Technology, Leibnizstrasse 6, D-38678 Clausthal-Zellerfeld, Germany
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20
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Watkins RD, Buckarma EH, Tomlinson JL, McCabe CE, Yonkus JA, Werneburg NW, Bayer RL, Starlinger PP, Robertson KD, Wang C, Gores GJ, Smoot RL. SHP2 inhibition enhances Yes-associated protein mediated liver regeneration in murine partial hepatectomy models. JCI Insight 2022; 7:159930. [PMID: 35763355 PMCID: PMC9462473 DOI: 10.1172/jci.insight.159930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Disrupted liver regeneration following hepatectomy represents an “undruggable” clinical challenge associated with poor patient outcomes. Yes-associated protein (YAP), a transcriptional coactivator that is repressed by the Hippo pathway, is instrumental in liver regeneration. We have previously described an alternative, Hippo-independent mechanism of YAP activation mediated by downregulation of protein tyrosine phosphatase nonreceptor type 11 (PTPN11, also known as SHP2) inhibition. Herein, we examined the effects of YAP activation with a selective SHP1/SHP2 inhibitor, NSC-87877, on liver regeneration in murine partial hepatectomy models. In our studies, NSC-87877 led to accelerated hepatocyte proliferation, improved liver regeneration, and decreased markers of injury following partial hepatectomy. The effects of NSC-87877 were lost in mice with hepatocyte-specific Yap/Taz deletion, and this demonstrated dependence on these molecules for the enhanced regenerative response. Furthermore, administration of NSC-87877 to murine models of nonalcoholic steatohepatitis was associated with improved survival and decreased markers of injury after hepatectomy. Evaluation of transcriptomic changes in the context of NSC-87877 administration revealed reduction in fibrotic signaling and augmentation of cell cycle signaling. Cytoprotective changes included downregulation of Nr4a1, an apoptosis inducer. Collectively, the data suggest that SHP2 inhibition induces a pro-proliferative and cytoprotective enhancement of liver regeneration dependent on YAP.
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Affiliation(s)
- Ryan D Watkins
- Department of Surgery, Mayo Clinic, Rochester, United States of America
| | - EeeLN H Buckarma
- Department of Surgery, Mayo Clinic, Rochester, United States of America
| | | | - Chantal E McCabe
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, United States of America
| | - Jennifer A Yonkus
- Department of Surgery, Mayo Clinic, Rochester, United States of America
| | - Nathan W Werneburg
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States of America
| | - Rachel L Bayer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States of America
| | | | - Keith D Robertson
- Division of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, United States of America
| | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic, Rochester, United States of America
| | - Gregory J Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States of America
| | - Rory L Smoot
- Department of Surgery, Mayo Clinic, Rochester, United States of America
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21
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Song Y, Yang X, Wang S, Zhao M, Yu B. Crystallographic landscape of SHP2 provides molecular insights for SHP2 targeted drug discovery. Med Res Rev 2022; 42:1781-1821. [DOI: 10.1002/med.21890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/17/2022] [Accepted: 05/04/2022] [Indexed: 12/31/2022]
Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment Zhengzhou University 450000 Henan Zhengzhou China
| | - Xinyu Yang
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
| | - Shu Wang
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
| | - Min Zhao
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
| | - Bin Yu
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment Zhengzhou University 450000 Henan Zhengzhou China
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22
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Liang L, Liu H, Xing G, Deng C, Hua Y, Gu R, Lu T, Chen Y, Zhang Y. Accurate calculation of absolute free energy of binding for SHP2 allosteric inhibitors using free energy perturbation. Phys Chem Chem Phys 2022; 24:9904-9920. [PMID: 35416820 DOI: 10.1039/d2cp00405d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate prediction of binding affinity is a primary objective in structure-based drug discovery. A free energy perturbation (FEP) method based on molecular dynamics simulation shows great promise for protein-ligand binding affinity predictions. However, accurate calculation of binding affinity for allosteric inhibitors remains unknown and elusive, which hampers the discovery of allosteric inhibitors. Allosteric inhibitors exhibit several significant advantages over orthosteric inhibitors including higher specificity and lower side effects. Allosteric inhibitors against SHP2 are thought to be beneficial not only for diseases related to metabolism, but also for cancer, which make SHP2 a potential drug target. However, high structural sensitivity makes structural optimization of SHP2 allosteric inhibitors face challenges. Herein, we calculated the absolute binding free energy of SHP2 allosteric inhibitors using the FEP method by employing different λ-windows/simulation time sampling strategies. A simulation run with 32 λ-windows/64 ps sampling strategy delivered an excellent correlation (r = 0.96) and an unprecedented low mean absolute error of 0.5 kcal mol-1 between predicted binding free energies and experimental ones, outperforming the MM/PBSA method. Our study demonstrates the possibility to accurately calculate the absolute binding free energy of allosteric inhibitors using FEP, which offers exciting prospects for the discovery of more effective allosteric inhibitors.
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Affiliation(s)
- Li Liang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
| | - Guomeng Xing
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
| | - Chenglong Deng
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
| | - Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
| | - Rui Gu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China. .,State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
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23
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Engineered Allosteric Regulation of Protein Function. J Mol Biol 2022; 434:167620. [PMID: 35513109 DOI: 10.1016/j.jmb.2022.167620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/27/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022]
Abstract
Allosteric regulation of proteins has been utilized to study various aspects of cell signaling, from unicellular events to organism-wide phenotypes. However, traditional methods of allosteric regulation, such as constitutively active mutants and inhibitors, lack tight spatiotemporal control. This often leads to unintended signaling consequences that interfere with data interpretation. To overcome these obstacles, researchers employed protein engineering approaches that enable tight control of protein function through allosteric mechanisms. These methods provide high specificity as well as spatial and temporal precision in regulation of protein activity in vitro and in vivo. In this review, we focus on the recent advancements in engineered allosteric regulation and discuss the various bioengineered allosteric techniques available now, from chimeric GPCRs to chemogenetic and optogenetic switches. We highlight the benefits and pitfalls of each of these techniques as well as areas in which future improvements can be made. Additionally, we provide a brief discussion on implementation of engineered allosteric regulation approaches, demonstrating that these tools can shed light on elusive biological events and have the potential to be utilized in precision medicine.
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24
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Kanumuri R, Pasupuleti SK, Burns SS, Ramdas B, Kapur R. Targeting SHP2 phosphatase in hematological malignancies. Expert Opin Ther Targets 2022; 26:319-332. [PMID: 35503226 PMCID: PMC9239432 DOI: 10.1080/14728222.2022.2066518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/12/2022] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Src homology-2-containing protein tyrosine phosphatase 2 (SHP2) is a ubiquitously expressed, non-receptor protein tyrosine phosphatase encoded by the PTPN11 gene. Gain-of-function (GOF) mutations in PTPN11 are associated with the development of various hematological malignancies and Noonan syndrome with multiple lentigines (NS-ML). Preclinical studies performed with allosteric SHP2 inhibitors and combination treatments of SHP2 inhibitors with inhibitors of downstream regulators (such as MEK, ERK, and PD-1/PD-L1) demonstrate improved antitumor benefits. However, the development of novel SHP2 inhibitors is necessary to improve the therapeutic strategies for hematological malignancies and tackle drug resistance and disease relapse. AREAS COVERED This review examines the structure of SHP2, its function in various signaling cascades, the consequences of constitutive activation of SHP2 and potential therapeutic strategies to treat SHP2-driven hematological malignancies. EXPERT OPINION While SHP2 inhibitors have exhibited promise in preclinical trials, numerous challenges remain in translation to the clinic, including drug resistance. Although PROTAC-based SHP2 degraders show better efficacy than SHP2 inhibitors, novel strategies need to be designed to improve SHP2-specific therapies in hematologic malignancies. Genome-wide CRISPR screening should also be used to identify molecules that confer resistance to SHP2 inhibitors. Targeting these molecules together with SHP2 can increase the target specificity and reduce drug resistance.
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Affiliation(s)
- Rahul Kanumuri
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Santhosh Kumar Pasupuleti
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sarah S Burns
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Baskar Ramdas
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Reuben Kapur
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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25
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Wang M, Li T, Ouyang Z, Tang K, Zhu Y, Song C, Sun H, Yu B, Ji X, Sun Y. SHP2 allosteric inhibitor TK-453 alleviates psoriasis-like skin inflammation in mice via inhibition of IL-23/Th17 axis. iScience 2022; 25:104009. [PMID: 35310939 PMCID: PMC8927994 DOI: 10.1016/j.isci.2022.104009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/21/2022] [Accepted: 02/25/2022] [Indexed: 12/16/2022] Open
Abstract
SHP2 is the first oncogenic tyrosine phosphatase encoded by PTPN11, which plays a significant regulatory role in cancer and inflammation-related diseases. Although SHP2 allosteric inhibitors have been used in phase I/II clinical trials for solid tumors, whether SHP2 inhibition alleviates psoriasis remains unclear. Here we expressed and purified SHP2 related proteins, and established an enzyme activity screening system for different conformations of SHP2. We launched an iterative medicinal chemistry program and identified the lead compound, TK-453. Importantly, TK-453 possessed stronger affinity with SHP2 than SHP099, evidenced by the cocrystal structure of SHP2/TK-453, revealing that the additional aryl-S-aryl bridge in TK-453 induces a 1.8 Å shift of the dichlorophenyl ring and an approximate 20° deviation of the pyrazine ring plane relative to SHP099. Furthermore, TK-453 significantly ameliorated imiquimod-triggered skin inflammation in mice via inhibition of the IL-23/Th17 axis, proving that SHP2 is a potential therapeutic target for psoriasis. We identify a SHP2 allosteric inhibitor TK-453, which has a stronger affinity with SHP2 Cocrystal structure shows that TK-453 occupies the allosteric pocket of SHP2 TK-453 alleviates psoriasis-like skin inflammation in mice SHP2 inhibitor provides a new strategy for the treatment of psoriasis
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26
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Kong J, Long YQ. Recent advances in the discovery of protein tyrosine phosphatase SHP2 inhibitors. RSC Med Chem 2022; 13:246-257. [PMID: 35434626 PMCID: PMC8942255 DOI: 10.1039/d1md00386k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/14/2022] [Indexed: 01/17/2023] Open
Abstract
Src homology 2 domain-containing protein tyrosine phosphatase (SHP2) is a non-receptor protein tyrosine phosphatase encoded by the Ptpn11 gene, which regulates cell growth, differentiation and apoptosis via modulating various signaling pathways, such as the RAS/ERK signaling pathway, and participates in the PD-1/PD-L1 pathway governing immune surveillance. It has been recognized as a breakthrough antitumor therapeutic target. Besides, numerous studies have shown that SHP2 plays an important role in the regulation of inflammatory diseases. However, inhibitors targeting the active site of SHP2 lack drug-likeness due to their low selectivity and poor bioavailability, thus none has advanced to clinical development. Recently, allosteric inhibitors that stabilize the inactive conformation of SHP2 have achieved breakthrough progress, providing the clinical proof for the druggability of SHP2 as an antitumor drug target. This paper reviews the recently reported design and discovery of SHP2 small molecule inhibitors, focused on the structure-activity relationship (SAR) analysis of several representative SHP2 inhibitors, outlining the evolution and therapeutic potential of the small molecule inhibitors targeting SHP2.
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Affiliation(s)
- Jiao Kong
- Laboratory of Medicinal Chemical Biology, Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University Medical College Suzhou 215123 China
| | - Ya-Qiu Long
- Laboratory of Medicinal Chemical Biology, Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University Medical College Suzhou 215123 China
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27
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Tang K, Zhao M, Wu YH, Wu Q, Wang S, Dong Y, Yu B, Song Y, Liu HM. Structure-based design, synthesis and biological evaluation of aminopyrazines as highly potent, selective, and cellularly active allosteric SHP2 inhibitors. Eur J Med Chem 2022; 230:114106. [PMID: 35063735 DOI: 10.1016/j.ejmech.2022.114106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 11/26/2022]
Abstract
Src homology-2-containing protein tyrosine phosphatase 2 (SHP2) encoded by the proto-oncogene PTPN11 is the first identified non-receptor protein tyrosine phosphatase. SHP2 dysregulation contributes to the pathogenesis of different cancers, making SHP2 a promising therapeutic target for cancer therapy. In this article, we report the structure-guided design based on the well-characterized SHP2 inhibitor SHP099, extensive structure-activity relationship studies (SARs) of aminopyrazines, biochemical characterization and cellular potency. These medicinal chemistry efforts lead to the discovery of the lead compound TK-453, which potently inhibits SHP2 (SHP2WT IC50 = 0.023 μM, ΔTm = 7.01 °C) in a reversible and noncompetitive manner. TK-453 exhibits high selectivity over SHP2PTP, SHP1 and PTP1B, and may bind at the "tunnel" allosteric site of SHP2 as SHP099. As the key pharmacophore, the aminopyrazine scaffold not only reorganizes the cationic-π stacking interaction with R111 via the novel hydrogen bond interaction between the S atom of thioether linker and T219, but also mediates a hydrogen bond with E250. In vitro studies indicate that TK-453 inhibits proliferation of HeLa, KYSE-70 and THP-1 cells moderately and induces apoptosis of Hela cells. Further mechanistic studies suggest that TK-453 can decrease the phosphorylation levels of AKT and Erk1/2 in HeLa and KYSE-70 cells. Collectively, TK-453 is a highly potent, selective, and cellularly active allosteric SHP2 inhibitor that modulates the phosphorylation of SHP2-mediated AKT and Erk cell signaling pathways by inhibiting the phosphatase activity of SHP2.
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Affiliation(s)
- Kai Tang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Min Zhao
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Ya-Hong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Qiong Wu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Shu Wang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Yu Dong
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China.
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28
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Song Y, Wang S, Zhao M, Yang X, Yu B. Strategies Targeting Protein Tyrosine Phosphatase SHP2 for Cancer Therapy. J Med Chem 2022; 65:3066-3079. [PMID: 35157464 DOI: 10.1021/acs.jmedchem.1c02008] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The protein tyrosine phosphatase SHP2 encoded by PTPN11 is a promising therapeutic target for cancer therapy, while the multifaceted roles of SHP2 complicate the drug discovery targeting SHP2. Given the biological significance of SHP2, strategies targeting SHP2 have been developed in recent years. To date, eight SHP2 inhibitors have advanced into clinical trials as mono- or combined therapy for treating solid tumors or adaptive resistant cancers. In this Perspective, we briefly summarize the strategies targeting SHP2 including inhibitors, activators, and proteolysis-targeting chimera (PROTAC) degraders. Besides, targeting the protein-protein interactions between SHP2 and other adaptor proteins is also discussed. Finally, we also highlight the target- and pathway-dependent combination strategies of SHP2 for cancer therapy. This Perspective may provide a timely and updated overview on the strategies targeting SHP2 for cancer therapy.
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China.,State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100000, China
| | - Shu Wang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Min Zhao
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Xinyu Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China.,State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100000, China
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29
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Ma Y, Li WY, Sun T, Zhang L, Lu XH, Yang B, Wang RL. Structure-based discovery of a specific SHP2 inhibitor with enhanced blood-brain barrier penetration from PubChem database. Bioorg Chem 2022; 121:105648. [PMID: 35180489 DOI: 10.1016/j.bioorg.2022.105648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/20/2022]
Abstract
The thiophene [2,3-d]pyrimidine structure-like small molecules were discovered from structure-based virtual screening of 1 billion compounds. Base on enzyme activity assay results, a SHP2-specific molecule inhibitor Comp#2 with IC50 of 1.174 μM, 85-fold more selective for SHP2 than the highly related SHP1 (IC50 > 100 μM). The compound can effectively inhibit SHP2-mediated cell signaling and cancer cell proliferation, including cervix cancer, human pancreatic cancer, large cell lung cancer, and mouse glioma cell. Moreover, the in vivo assay indicated that Comp#2 could inhibit cervix cancer tumors growth in BABL/c mice. This work has shown the specific SHP2 inhibitor can inhibit glioblastoma growth in vivo.
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Affiliation(s)
- Ying Ma
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, People's Republic of China
| | - Wei-Ya Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, People's Republic of China
| | - Ting Sun
- Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China
| | - Ling Zhang
- School of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei 050015, China
| | - Bing Yang
- School of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China.
| | - Run-Ling Wang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, People's Republic of China.
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30
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HAN N, SU Y, GUO M, YU L. Retinal SHP2 silencing alleviates diabetic retinopathy via suppressing inflammatory response and oxidative stress by regulating YAP1 activity. Exp Anim 2022; 71:376-384. [PMID: 35400714 PMCID: PMC9388342 DOI: 10.1538/expanim.21-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Diabetic retinopathy (DR) is the prevalent microvascular complication of diabetes mellitus (DM), and it may lead to permanent blindness. The previous publication has indicated that both
inflammatory response and oxidative stress are critical factors involved in DR progression, however, the accurate regulatory mechanism remains to be revealed. Src homology region 2
(SH2)-containing protein tyrosine phosphatase 2 (SHP2), a member of the protein tyrosine phosphatase family, was reported to play a role in diabetic nephropathy, whereas its function in DR
was unknown and required further exploration. The level of phosphorylated, not the total, SHP2 increased in the retinas of rats with streptozotocin injection-induced DM. Further, the
intravitreal injection of SHP2 shRNA lentivirus alleviated retinal pathological changes, and inhibited inflammatory response and oxidative stress, which were accompanied with Yes-associated
protein 1 (YAP1) deactivation in DR rats. Additional co-immunoprecipitation results confirmed the interaction of SHP2 and YAP1. Collectively, our data preliminarily show that DR
amelioration-induced by SHP2 inhibition in rats may attribute to the deactivation of YAP1 pathway.
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Affiliation(s)
- Ning HAN
- Department of Ophthalmology, The Second Hospital of Jilin University
| | - Ying SU
- Department of Ophthalmology, Liaoyuan People’s Hospital
| | - Mi GUO
- Department of Ophthalmology, Baotou Eye Hospital
| | - Li YU
- Department of Ophthalmology, The Second Hospital of Jilin University
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31
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Li J, Xie J, Godec A, Weninger KR, Liu C, Smith JC, Hong L. Non-ergodicity of a globular protein extending beyond its functional timescale. Chem Sci 2022; 13:9668-9677. [PMID: 36091909 PMCID: PMC9400594 DOI: 10.1039/d2sc03069a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble. Here, by performing single-molecule fluorescence resonance energy transfer (smFRET) experiments and molecular dynamics (MD) simulations of a multi-domain globular protein, cytoplasmic protein-tyrosine phosphatase (SHP2), we demonstrate that the functional inter-domain motion is observationally non-ergodic over the time spans 10−12 to 10−7 s and 10−1 to 102 s. The difference between observational non-ergodicity and simple non-convergence is discussed. In comparison, a single-strand DNA of similar size behaves ergodically with an energy landscape resembling a one-dimensional linear chain. The observed non-ergodicity results from the hierarchical connectivity of the high-dimensional energy landscape of the protein molecule. As the characteristic time for the protein to conduct its dephosphorylation function is ∼10 s, our findings suggest that, due to the non-ergodicity, individual, seemingly identical protein molecules can be dynamically and functionally different. Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble.![]()
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Affiliation(s)
- Jun Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - JingFei Xie
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Aljaž Godec
- Mathematical BioPhysics Group, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Keith R. Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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32
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Li JC, Gao WX, Liu MC, Zhou YB, Wu HY. α-Selective C(sp 3)-H Thio/Selenocyanation of Ketones with Elemental Chalcogen. J Org Chem 2021; 86:17294-17306. [PMID: 34784197 DOI: 10.1021/acs.joc.1c02431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A facile method is disclosed for the synthesis of α-thio/selenocyanato ketones through regioselective C-H thio/selenocyanation of ketones. The advantages include the use of easily available starting materials, high efficiency, simple operation, and easy scale-up. Control experiments provide evidence that the reaction proceeded via a radical way, while kinetic isotope effect experiments reveal that the cleavage of the C-H bond serves as the rate-limiting step.
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Affiliation(s)
- Jin-Cheng Li
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Wen-Xia Gao
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Miao-Chang Liu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Yun-Bing Zhou
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Hua-Yue Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
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Liu M, Gao S, Elhassan RM, Hou X, Fang H. Strategies to overcome drug resistance using SHP2 inhibitors. Acta Pharm Sin B 2021; 11:3908-3924. [PMID: 35024315 PMCID: PMC8727779 DOI: 10.1016/j.apsb.2021.03.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
Encoded by PTPN11, the SHP2 (Src homology-2 domain-containing protein tyrosine phosphatase-2) is widely recognized as a carcinogenic phosphatase. As a promising anti-cancer drug target, SHP2 regulates many signaling pathways such as RAS-RAF-ERK, PI3K-AKT and JAK-STAT. Meanwhile, SHP2 plays a significant role in regulating immune cell function in the tumor microenvironment. Heretofore, five SHP2 allosteric inhibitors have been recruited in clinical studies for the treatment of cancer. Most recently, studies have proved the therapeutic potential of SHP2 inhibitor in overcoming drug resistance of kinase inhibitors and programmed cell death-1 (PD-1) blockade. Herein, we review the structure, function and small molecular inhibitors of SHP2, and highlight recent progress in overcoming drug resistance using SHP2 inhibitor. We hope this review would facilitate the future clinical development of SHP2 inhibitors.
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Affiliation(s)
| | | | | | - Xuben Hou
- Corresponding author. Tel./fax: +86 531 88381168.
| | - Hao Fang
- Corresponding author. Tel./fax: +86 531 88381168.
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Elhassan RM, Hou X, Fang H. Recent advances in the development of allosteric protein tyrosine phosphatase inhibitors for drug discovery. Med Res Rev 2021; 42:1064-1110. [PMID: 34791703 DOI: 10.1002/med.21871] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 09/26/2021] [Accepted: 10/24/2021] [Indexed: 01/07/2023]
Abstract
Protein tyrosine phosphatases (PTPs) superfamily catalyzes tyrosine de-phosphorylation which affects a myriad of cellular processes. Imbalance in signal pathways mediated by PTPs has been associated with development of many human diseases including cancer, metabolic, and immunological diseases. Several compelling evidence suggest that many members of PTP family are novel therapeutic targets. However, the clinical development of conventional PTP-based active-site inhibitors originally was hampered by the poor selectivity and pharmacokinetic properties. In this regard, PTPs has been widely dismissed as "undruggable." Nonetheless, allosteric modulation has become increasingly an influential and alternative approach that can be exploited for drug development against PTPs. Unlike active-site inhibitors, allosteric inhibitors exhibit a remarkable target-selectivity, drug-likeness, potency, and in vivo activity. Intriguingly, there has been a high interest in novel allosteric PTPs inhibitors within the last years. In this review, we focus on the recent advances of allosteric inhibitors that have been explored in drug discovery and have shown an excellent result in the development of PTPs-based therapeutics. A special emphasis is placed on the structure-activity relationship and molecular mechanistic studies illustrating applications in chemical biology and medicinal chemistry.
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Affiliation(s)
- Reham M Elhassan
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
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Bobone S, Pannone L, Biondi B, Solman M, Flex E, Canale VC, Calligari P, De Faveri C, Gandini T, Quercioli A, Torini G, Venditti M, Lauri A, Fasano G, Hoeksma J, Santucci V, Cattani G, Bocedi A, Carpentieri G, Tirelli V, Sanchez M, Peggion C, Formaggio F, den Hertog J, Martinelli S, Bocchinfuso G, Tartaglia M, Stella L. Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein-Protein Interactions. J Med Chem 2021; 64:15973-15990. [PMID: 34714648 PMCID: PMC8591604 DOI: 10.1021/acs.jmedchem.1c01371] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in cell signaling and represents a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhibitors target the catalytic site or an allosteric pocket but lack specificity or are ineffective for disease-associated SHP2 mutants. Considering that pathogenic lesions cause signaling hyperactivation due to increased levels of SHP2 association with cognate proteins, we developed peptide-based molecules with nanomolar affinity for the N-terminal Src homology domain of SHP2, good selectivity, stability to degradation, and an affinity for pathogenic variants of SHP2 that is 2-20 times higher than for the wild-type protein. The best peptide reverted the effects of a pathogenic variant (D61G) in zebrafish embryos. Our results provide a novel route for SHP2-targeted therapies and a tool for investigating the role of protein-protein interactions in the function of SHP2.
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Affiliation(s)
- Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Luca Pannone
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
| | - Maja Solman
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Elisabetta Flex
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Viviana Claudia Canale
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Chiara De Faveri
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Tommaso Gandini
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Andrea Quercioli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giuseppe Torini
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Jelmer Hoeksma
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Valerio Santucci
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giada Cattani
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Alessio Bocedi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giovanna Carpentieri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Valentina Tirelli
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Massimo Sanchez
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Jeroen den Hertog
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Simone Martinelli
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
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Wang F, Yang W, Li Z, Zhou B. Studies on molecular mechanism between SHP2 and pyridine derivatives by 3D-QSAR, molecular docking and MD simulations. JOURNAL OF SAUDI CHEMICAL SOCIETY 2021. [DOI: 10.1016/j.jscs.2021.101346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Double-edged roles of protein tyrosine phosphatase SHP2 in cancer and its inhibitors in clinical trials. Pharmacol Ther 2021; 230:107966. [PMID: 34403682 DOI: 10.1016/j.pharmthera.2021.107966] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022]
Abstract
Phosphorylation is a reversible post-translational modification regulated by phosphorylase and dephosphorylase to mediate important cellular events. Src homology-2-containing protein tyrosine phosphatase 2 (SHP2) encoded by PTPN11 is the first identified oncogenic protein in protein tyrosine phosphatases family. Serving as a convergent node, SHP2 is involved in multiple cascade signaling pathways including Ras-Raf-MEK-ERK, PI3K-AKT, JAK-STAT and PD-1/PD-L1 pathways. Especially, the double-edged roles of SHP2 based on the substrate specificity in various biological contexts dramatically increase the effect complexity in different SHP2-associated diseases. Evidences suggest that by collaborating with other mutations in associated pathways, dysregulation of SHP2 contributes to the pathogenesis of different cancers, making SHP2 a promising therapeutic target for cancer treatment. SHP2 can either act as oncogenic factor or tumor suppressor in different diseases, and both the conserved catalytic dephosphorylation mechanism and the unique allosteric regulation mechanism of SHP2 provide opportunities for the development of SHP2 inhibitors and activators. To date, several small-molecule SHP2 inhibitors have advanced into clinical trials for mono- or combined therapy of cancers. Moreover, SHP2 activators and proteolysis-targeting chimera (PROTAC)-based degraders also display therapeutic promise. In this review, we comprehensively summarize the overall structures, regulation mechanisms, double-edged roles of SHP2 in both physiological and carcinogenic pathways, and SHP2 inhibitors in clinical trials. SHP2 activators and degraders are also briefly discussed. This review aims to provide in-depth understanding of the biological roles of SHP2 and highlight therapeutic potential of targeting SHP2.
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38
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Yang B, Zhou J, Wang F, Hu XW, Shi Y. Pyrazoline derivatives as tubulin polymerization inhibitors with one hit for Vascular Endothelial Growth Factor Receptor 2 inhibition. Bioorg Chem 2021; 114:105134. [PMID: 34246970 DOI: 10.1016/j.bioorg.2021.105134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/06/2021] [Accepted: 06/26/2021] [Indexed: 02/07/2023]
Abstract
In this work, to check the effect of the transposition of the rings in typical patterns, a series of pyrazoline derivatives 3a-3t bearing the characteristic 3,4,5-trimethoxy phenyl and thiophene moieties were synthesized and evaluated as tubulin polymerization inhibitors. Basically, as the concise output of our design, a majority of the synthesized compounds showed potency in inhibiting the tubulin polymerization. The top hit, 3q, exhibited potent anti-proliferation activity on cancer cell lines. It was comparable on tubulin-polymerization inhibition with the positive control Colchicine but lower toxic. The VEGFR2 inhibitory potency was introduced occasionally. The flow cytometry assay confirmed the apoptotic procedure and the confocal imaging revealed the tubulin-microtubule dynamics pattern. The anti-cancer mechanism of 3q was similar to Colchicine but not exactly the same on forming multi-polar spindles. The docking simulation visualized the possible binding patterns of 3q into tubulin and VEGFR2, respectively. The results inferred that further investigations on the transposition of the rings might lead to the improvement of tubulin polymerization inhibitory activity and the steadily introduction of the VEGFR2 inhibition.
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Affiliation(s)
- Bing Yang
- School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, China.
| | - Jiahua Zhou
- School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, China
| | - Fa Wang
- School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, China
| | - Xiao-Wei Hu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong 276005, China
| | - Yujun Shi
- School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, China.
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Wu J, Zhang H, Zhao G, Wang R. Allosteric Inhibitors of SHP2: An Updated Patent Review (2015-2020). Curr Med Chem 2021; 28:3825-3842. [PMID: 32988341 DOI: 10.2174/1568011817666200928114851] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 11/22/2022]
Abstract
Srchomology-2-domain-containing PTP 2 (SHP2) is a nonreceptor phosphatase encoded by the PTPN11 gene. Over expression of SHP2 is associated with various human diseases, such as Noonan syndrome, LEOPARD syndrome, and cancers. To overcome the shortcomings of existing orthosteric inhibitors, novel inhibitors targeting the allosteric site of SHP2 with high selectivity and low toxicity are under development. This paper reviews allosteric inhibitors of SHP2 published in patents from 2015 to 2020. The molecules are classified according to the chemical structure of the central core. SHP2 has long been considered as an 'undruggable' protein. Fortunately, a critical breakthrough was made by researchers from Novartis AG Ltd., who identified SHP099 as a highly potent, selective, soluble, and orally bioavailable SHP2 allosteric inhibitor. Currently, there are several allosteric inhibitors of SHP2 in clinical development. However, drug resistance is still a major challenge. The combination of SHP2 allosteric inhibitors and immunotherapy drugs or molecular targeted drugs is emerging as a promising therapeutic strategy against drug resistance.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, No. 22, Qixiangtai Road, Heping District, Tianjin 300070, China
| | - Huan Zhang
- Department of Pharmacy, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Guilong Zhao
- The Institute of Drug Discovery and Development, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, No. 22, Qixiangtai Road, Heping District, Tianjin 300070, China
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40
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Guo Y, Xu Y, Dong X, Zhang J. Cross the Undruggable Barrier, the Development of SHP2 Inhibitors: From Catalytic Site Inhibitors to Allosteric Inhibitors. ChemistrySelect 2021. [DOI: 10.1002/slct.202100186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yu Guo
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Yaping Xu
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Jianjun Zhang
- Department of Pharmacy Institution The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine) Hangzhou 310006 P.R. China
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41
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Pudewell S, Wittich C, Kazemein Jasemi NS, Bazgir F, Ahmadian MR. Accessory proteins of the RAS-MAPK pathway: moving from the side line to the front line. Commun Biol 2021; 4:696. [PMID: 34103645 PMCID: PMC8187363 DOI: 10.1038/s42003-021-02149-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
Health and disease are directly related to the RTK-RAS-MAPK signalling cascade. After more than three decades of intensive research, understanding its spatiotemporal features is afflicted with major conceptual shortcomings. Here we consider how the compilation of a vast array of accessory proteins may resolve some parts of the puzzles in this field, as they safeguard the strength, efficiency and specificity of signal transduction. Targeting such modulators, rather than the constituent components of the RTK-RAS-MAPK signalling cascade may attenuate rather than inhibit disease-relevant signalling pathways.
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Affiliation(s)
- Silke Pudewell
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Christoph Wittich
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Neda S. Kazemein Jasemi
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Farhad Bazgir
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Mohammad R. Ahmadian
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
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42
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Nian Q, Zeng J, He L, Chen Y, Zhang Z, Rodrigues-Lima F, Zhao L, Feng X, Shi J. A small molecule inhibitor targeting SHP2 mutations for the lung carcinoma. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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43
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New Insights into YES-Associated Protein Signaling Pathways in Hematological Malignancies: Diagnostic and Therapeutic Challenges. Cancers (Basel) 2021; 13:cancers13081981. [PMID: 33924049 PMCID: PMC8073623 DOI: 10.3390/cancers13081981] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/03/2021] [Accepted: 04/16/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary YES-associated protein (YAP) is a co-transcriptional activator that binds to transcriptional factors to increase the rate of transcription of a set of genes, and it can intervene in the onset and progression of different tumors. Most of the data in the literature refer to the effects of the YAP system in solid neoplasms. In this review, we analyze the possibility that YAP can also intervene in hematological neoplasms such as lymphomas, multiple myeloma, and acute and chronic leukemias, modifying the phenomena of cell proliferation and cell death. The possibilities of pharmacological intervention related to the YAP system in an attempt to use its modulation therapeutically are also discussed. Abstract The Hippo/YES-associated protein (YAP) signaling pathway is a cell survival and proliferation-control system with its main activity that of regulating cell growth and organ volume. YAP operates as a transcriptional coactivator in regulating the onset, progression, and treatment response in numerous human tumors. Moreover, there is evidence suggesting the involvement of YAP in the control of the hematopoietic system, in physiological conditions rather than in hematological diseases. Nevertheless, several reports have proposed that the effects of YAP in tumor cells are cell-dependent and cell-type-determined, even if YAP usually interrelates with extracellular signaling to stimulate the onset and progression of tumors. In the present review, we report the most recent findings in the literature on the relationship between the YAP system and hematological neoplasms. Moreover, we evaluate the possible therapeutic use of the modulation of the YAP system in the treatment of malignancies. Given the effects of the YAP system in immunosurveillance, tumorigenesis, and chemoresistance, further studies on interactions between the YAP system and hematological malignancies will offer very relevant information for the targeting of these diseases employing YAP modifiers alone or in combination with chemotherapy drugs.
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Sobhani N, Tardiel-Cyril DR, Davtyan A, Generali D, Roudi R, Li Y. CTLA-4 in Regulatory T Cells for Cancer Immunotherapy. Cancers (Basel) 2021; 13:1440. [PMID: 33809974 PMCID: PMC8005092 DOI: 10.3390/cancers13061440] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have obtained durable responses in many cancers, making it possible to foresee their potential in improving the health of cancer patients. However, immunotherapies are currently limited to a minority of patients and there is a need to develop a better understanding of the basic molecular mechanisms and functions of pivotal immune regulatory molecules. Immune checkpoint cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and regulatory T (Treg) cells play pivotal roles in hindering the anticancer immunity. Treg cells suppress antigen-presenting cells (APCs) by depleting immune stimulating cytokines, producing immunosuppressive cytokines and constitutively expressing CTLA-4. CTLA-4 molecules bind to CD80 and CD86 with a higher affinity than CD28 and act as competitive inhibitors of CD28 in APCs. The purpose of this review is to summarize state-of-the-art understanding of the molecular mechanisms underlining CTLA-4 immune regulation and the correlation of the ICI response with CTLA-4 expression in Treg cells from preclinical and clinical studies for possibly improving CTLA-4-based immunotherapies, while highlighting the knowledge gap.
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Affiliation(s)
- Navid Sobhani
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Dana Rae Tardiel-Cyril
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Aram Davtyan
- Atomwise, 717 Market St, San Francisco, CA 94103, USA;
| | - Daniele Generali
- Department of Medical, Surgery and Health Sciences, University of Trieste, 34147 Trieste, Italy;
| | - Raheleh Roudi
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA;
| | - Yong Li
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX 77030, USA;
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45
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Tao Y, Xie J, Zhong Q, Wang Y, Zhang S, Luo F, Wen F, Xie J, Zhao J, Sun X, Long H, Ma J, Zhang Q, Long J, Fang X, Lu Y, Li D, Li M, Zhu J, Sun B, Li G, Diao J, Liu C. A novel partially open state of SHP2 points to a "multiple gear" regulation mechanism. J Biol Chem 2021; 296:100538. [PMID: 33722610 PMCID: PMC8054191 DOI: 10.1016/j.jbc.2021.100538] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 03/03/2021] [Accepted: 03/10/2021] [Indexed: 11/14/2022] Open
Abstract
The protein tyrosine phosphatase SHP2 mediates multiple signal transductions in various cellular pathways, controlled by a variety of upstream inputs. SHP2 dysregulation is causative of different types of cancers and developmental disorders, making it a promising drug target. However, how SHP2 is modulated by its different regulators remains largely unknown. Here, we use single-molecule fluorescence resonance energy transfer and molecular dynamics simulations to investigate this question. We identify a partially open, semiactive conformation of SHP2 that is intermediate between the known open and closed states. We further demonstrate a “multiple gear” regulatory mechanism, in which different activators (e.g., insulin receptor substrate-1 and CagA), oncogenic mutations (e.g., E76A), and allosteric inhibitors (e.g., SHP099) can shift the equilibrium of the three conformational states and regulate SHP2 activity to different levels. Our work reveals the essential role of the intermediate state in fine-tuning the activity of SHP2, which may provide new opportunities for drug development for relevant cancers.
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Affiliation(s)
- Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Jingfei Xie
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Qinglu Zhong
- University of the Chinese Academy of Sciences, Beijing, China; Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yongyao Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Feng Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Fengcai Wen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jingjing Xie
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Jiawei Zhao
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoou Sun
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Houfang Long
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qian Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jiangang Long
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ying Lu
- University of the Chinese Academy of Sciences, Beijing, China; Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Li
- University of the Chinese Academy of Sciences, Beijing, China; Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Jidong Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guohui Li
- University of the Chinese Academy of Sciences, Beijing, China; Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China.
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Song Y, Zhao M, Wu Y, Yu B, Liu HM. A multifunctional cross-validation high-throughput screening protocol enabling the discovery of new SHP2 inhibitors. Acta Pharm Sin B 2021; 11:750-762. [PMID: 33777680 PMCID: PMC7982506 DOI: 10.1016/j.apsb.2020.10.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/01/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
The protein tyrosine phosphatase Src homology phosphotyrosyl phosphatase 2 (SHP2) is implicated in various cancers, and targeting SHP2 has become a promising therapeutic approach. We herein described a robust cross-validation high-throughput screening protocol that combined the fluorescence-based enzyme assay and the conformation-dependent thermal shift assay for the discovery of SHP2 inhibitors. The established method can effectively exclude the false positive SHP2 inhibitors with fluorescence interference and was also successfully employed to identify new protein tyrosine phosphatase domain of SHP2 (SHP2-PTP) and allosteric inhibitors. Of note, this protocol showed potential for identifying SHP2 inhibitors against cancer-associated SHP2 mutation SHP2-E76A. After initial screening of our in-house compound library (∼2300 compounds), we identified 4 new SHP2-PTP inhibitors (0.17% hit rate) and 28 novel allosteric SHP2 inhibitors (1.22% hit rate), of which SYK-85 and WS-635 effectively inhibited SHP2-PTP (SYK-85: IC50 = 0.32 μmol/L; WS-635: IC50 = 4.13 μmol/L) and thus represent novel scaffolds for designing new SHP2-PTP inhibitors. TK-147, an allosteric inhibitor, inhibited SHP2 potently (IC50 = 0.25 μmol/L). In structure, TK-147 could be regarded as a bioisostere of the well characterized SHP2 inhibitor SHP-099, highlighting the essential structural elements for allosteric inhibition of SHP2. The principle underlying the cross-validation protocol is potentially feasible to identify allosteric inhibitors or those inactivating mutants of other proteins.
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Key Words
- AKT, protein kinase B
- ALK, anaplastic lymphoma kinase
- AML, acute myelogenous leukemia
- Allosteric inhibitors
- BTLA, B and T lymphocyte attenuator
- Bis-tris, bis-(2-hydroxyethyl)amino-tris(hydroxymethyl)methane
- DTT, dithiothreitol
- DiFMU, 6,8-difluoro-4-methylumbelliferyl hydroxid
- DiFMUP, 6,8-difluoro-4-methylumbelliferyl phosphate
- Enzyme assay
- FI, fluorescence intensity
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- HTS, high-throughput screening
- High-throughput screening
- IC50, half maximal inhibitory concentration
- JAK, janus kinase
- JMML, juvenile myelomonocytic leukaemia
- LB, lysogeny broth
- LOC, ligand only control
- LS, LEOPARD syndrome
- MAPK, mitogen-activated protein kinase
- MEK, extracellular regulated protein kinase kinases
- NPC, no protein control
- NS, Noonan syndrome
- OD, optical density
- PD-1, programmed death 1
- PI3K, phosphatidylinositol 3 kinase
- PMSF, phenylmethanesulfonyl fluoride
- PTP, protein tyrosine phosphatase
- R2, coefficient of determination
- RAS, rat sarcoma
- S/B, signal over background
- SD, standard deviation
- SDS-PAGE, sodium dodecyl sulphate polyacyrlamide gel electrophoresis
- SH2, Src homology 2
- SHP2
- SHP2, Src homology phosphotyrosyl phosphatase 2
- SHP2-PTP, protein tyrosine phosphatase domain of Src homology phosphotyrosyl phosphatase 2
- SHP2-WT, wild type Src homology phosphotyrosyl phosphatase 2
- STAT, signal transducer and activator of transcription
- Thermal shift assay
- Tm, melting temperature
- p-IRS1, phosphorylated insulin receptor substrate 1
- ΔTm, melting temperature change
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Min Zhao
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
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Zheng M, Liu Y, Wu C, Yang K, Wang Q, Zhou Y, Chen L, Li H. Novel PROTACs for degradation of SHP2 protein. Bioorg Chem 2021; 110:104788. [PMID: 33706076 DOI: 10.1016/j.bioorg.2021.104788] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatase SHP2 is a member of PTPs family associated with cancer such as leukemia, non-small cell lung cancer, breast cancer, and so on. SHP2 is a promising target for drug development, and consequently it is of great significance to develop SHP2 inhibitors. Herein, we report CRBN-recruiting PROTAC molecules targeting SHP2 by connecting pomalidomide with SHP099, an allosteric inhibitor of SHP2. Among them, SP4 significantly inhibited the growth of Hela cells, compared with SHP099, its activity increased 100 times. In addition, it can significantly induce SHP2 degradation and cell apoptosis. Further study of SHP2-protac may have important significance for the treatment of SHP2 related diseases.
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Affiliation(s)
- Mengzhu Zheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yang Liu
- Department of Natural Products Chemistry, School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Canrong Wu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kaiyin Yang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qiqi Wang
- Department of Natural Products Chemistry, School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yirong Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Lixia Chen
- Department of Natural Products Chemistry, School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Hua Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Natural Products Chemistry, School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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48
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Targeting SHP2 as a therapeutic strategy for inflammatory diseases. Eur J Med Chem 2021; 214:113264. [PMID: 33582386 DOI: 10.1016/j.ejmech.2021.113264] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022]
Abstract
With the change of lifestyle and the acceleration of aging process, inflammatory diseases have increasingly become one of the most vital threats to global human health. SHP2 protein is a non-receptor tyrosine phosphatase encoded by PTPN11 gene, and it is widely expressed in various tissues and cells. Numerous studies have shown that SHP2 plays important roles in the regulation of inflammatory diseases, including cancer-related inflammation, neurodegenerative diseases and metabolic diseases. In this paper, the roles of SHP2 in inflammatory diseases of various physiological systems were reviewed. At the same time, the latest SHP2 inhibitors were summarized, which will hold a promise for the therapeutic potential in future.
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49
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Du S, Lu XH, Li WY, Li LP, Ma YC, Zhou L, Wu JW, Ma Y, Wang RL. Exploring the dynamic mechanism of allosteric drug SHP099 inhibiting SHP2 E69K. Mol Divers 2021; 25:1873-1887. [PMID: 33392964 DOI: 10.1007/s11030-020-10179-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
The E69K mutation is one of the most frequent protein tyrosine phosphatase-2 (SHP2) mutations in leukemia, and it can cause the increase in the protein activity. Recent studies have shown that the E69K mutation was fairly sensitive to the allosteric inhibitor of SHP2 (SHP099). However, the molecular mechanism of the allosteric drug SHP099 inhibiting SHP2E69K remains unclear. Thus, the molecular dynamic simulations and the post-dynamics analyses (RMSF, PCA, DCCM, RIN and the binding free energies) for SHP2WT, SHP2WT-SHP099, SHP2E69K and SHP2E69K-SHP099 were carried out, respectively. Owing to the strong binding affinity of SHP099 to residues Thr219 and Arg220, the flexibility of linker region (residues Val209-Arg231) was reduced. Moreover, the presence of SHP099 kept the autoinhibition state of the SHP2 protein through enhancing the interactions between the linker region and Q loop in PTP domain, such as Thr219/Val490, Thr219/Asn491, Arg220/Ile488 and Leu254/Asn491. In addition, it was found that the residues (Thr219, Arg220, Leu254 and Asn491) might be the key residues responsible for the conformational changes of protein. Overall, this study may provide an important basis for understanding how the SHP099 effectively inhibited the SHP2E69K activity at the molecular level.
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Affiliation(s)
- Shan Du
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, 050015, Hebei, China
| | - Wei-Ya Li
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Li-Peng Li
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Yang-Chun Ma
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Liang Zhou
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Jing-Wei Wu
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Ying Ma
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Run-Ling Wang
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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50
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Song Z, Wang M, Ge Y, Chen XP, Xu Z, Sun Y, Xiong XF. Tyrosine phosphatase SHP2 inhibitors in tumor-targeted therapies. Acta Pharm Sin B 2021; 11:13-29. [PMID: 33532178 PMCID: PMC7838030 DOI: 10.1016/j.apsb.2020.07.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022] Open
Abstract
Src homology containing protein tyrosine phosphatase 2 (SHP2) represents a noteworthy target for various diseases, serving as a well-known oncogenic phosphatase in cancers. As a result of the low cell permeability and poor bioavailability, the traditional inhibitors targeting the protein tyrosine phosphate catalytic sites are generally suffered from unsatisfactory applied efficacy. Recently, a particularly large number of allosteric inhibitors with striking inhibitory potency on SHP2 have been identified. In particular, few clinical trials conducted have made significant progress on solid tumors by using SHP2 allosteric inhibitors. This review summarizes the development and structure–activity relationship studies of the small-molecule SHP2 inhibitors for tumor therapies, with the purpose of assisting the future development of SHP2 inhibitors with improved selectivity, higher oral bioavailability and better physicochemical properties.
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Key Words
- ALK, anaplastic lymphoma kinase
- AML, acute myeloid leukemia
- Allosteric inhibitor
- B-ALL, B-cell acute lymphoblastic leukemia
- BTLA, B and T lymphocyte attenuator
- CADD, computer aided drug design
- CSF-1, colony stimulating factor-1
- CTLA-4, cytotoxic T lymphocyte-associated antigen-4
- EGFR, epidermal growth factor receptor
- ERK1/2, extracelluar signal-regulated kinase 1/2
- FLT3, Fms-like tyrosine kinase-3
- GAB2, Grb2-associated binding protein-2
- GRB2, growth factor receptor-bound protein 2
- HER2, human epidermal growth factor receptor-2
- HGF/SF, hepatocyte growth factor/scatter factor
- JAK, Janus kinase
- KRAS, v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
- MAPK, mitogen-activated protein kinase
- NLRP3, NLR family, pyrin domain containing protein 3
- PD-1/PDL-1, programmed cell death protein-1/programmed death ligand-1
- PDAC, pancreatic ductal adenocarcinoma
- PDX, patient-derived xenograft
- PI3K, phosphatidylinositol 3 kinase
- PTK, protein tyrosine kinase
- PTP, protein tyrosine phosphatase
- Phosphatase
- RAS, rat sarcoma protein
- RTKs, receptor tyrosine kinase inhibitors
- SAR, structure–activity relationship
- SBDD, structure-based drug design
- SCC, squamous cell carcinoma
- SCNA, somatic copy number change
- SHP2
- SHP2, Src homology containing protein tyrosine phosphatase 2
- STAT, signal transducers and activators of transcription
- Selectivity
- TIGIT, T-cell immunoglobulin and ITIM domain protein
- TKIs, tyrosine kinase inhibitors
- Tumor therapy
- hERG, human ether-a-go-go-related gene
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Affiliation(s)
- Zhendong Song
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Meijing Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yang Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xue-Ping Chen
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ziyang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiao-Feng Xiong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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