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Li Z, Qu N, Zhou J, Sun J, Ren Q, Meng J, Wang G, Wang R, Liu J, Chen Y, Zhang S, Zheng M, Li X. KinomeMETA: a web platform for kinome-wide polypharmacology profiling with meta-learning. Nucleic Acids Res 2024; 52:W489-W497. [PMID: 38752486 PMCID: PMC11223815 DOI: 10.1093/nar/gkae380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/21/2024] [Accepted: 04/26/2024] [Indexed: 07/06/2024] Open
Abstract
Kinase-targeted inhibitors hold promise for new therapeutic options, with multi-target inhibitors offering the potential for broader efficacy while minimizing polypharmacology risks. However, comprehensive experimental profiling of kinome-wide activity is expensive, and existing computational approaches often lack scalability or accuracy for understudied kinases. We introduce KinomeMETA, an artificial intelligence (AI)-powered web platform that significantly expands the predictive range with scalability for predicting the polypharmacological effects of small molecules across the kinome. By leveraging a novel meta-learning algorithm, KinomeMETA efficiently utilizes sparse activity data, enabling rapid generalization to new kinase tasks even with limited information. This significantly expands the repertoire of accurately predictable kinases to 661 wild-type and clinically-relevant mutant kinases, far exceeding existing methods. Additionally, KinomeMETA empowers users to customize models with their proprietary data for specific research needs. Case studies demonstrate its ability to discover new active compounds by quickly adapting to small dataset. Overall, KinomeMETA offers enhanced kinome virtual profiling capabilities and is positioned as a powerful tool for developing new kinase inhibitors and advancing kinase research. The KinomeMETA server is freely accessible without registration at https://kinomemeta.alphama.com.cn/.
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Affiliation(s)
- Zhaojun Li
- College of Computer and Information Engineering, Dezhou University, Dezhou City 253023, China
- Development Department, Suzhou Alphama Biotechnology Co., Ltd, Suzhou City 215000, China
| | - Ning Qu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jingyi Zhou
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jingjing Sun
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Qun Ren
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Jingyi Meng
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Guangchao Wang
- College of Computer and Information Engineering, Dezhou University, Dezhou City 253023, China
| | - Rongyan Wang
- College of Computer and Information Engineering, Dezhou University, Dezhou City 253023, China
| | - Jin Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yijie Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
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2
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Wang S, Xiong Y, Luo Y, Shen Y, Zhang F, Lan H, Pang Y, Wang X, Li X, Zheng X, Lu X, Liu X, Cheng Y, Wu T, Dong Y, Lu Y, Cui J, Jia X, Yang S, Wang L, Wang Y. Genome-wide CRISPR screens identify PKMYT1 as a therapeutic target in pancreatic ductal adenocarcinoma. EMBO Mol Med 2024; 16:1115-1142. [PMID: 38570712 PMCID: PMC11099189 DOI: 10.1038/s44321-024-00060-y] [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: 10/25/2023] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with an overall 5-year survival rate of <12% due to the lack of effective treatments. Novel treatment strategies are urgently needed. Here, PKMYT1 is identified through genome-wide CRISPR screens as a non-mutant, genetic vulnerability of PDAC. Higher PKMYT1 expression levels indicate poor prognosis in PDAC patients. PKMYT1 ablation inhibits tumor growth and proliferation in vitro and in vivo by regulating cell cycle progression and inducing apoptosis. Moreover, pharmacological inhibition of PKMYT1 shows efficacy in multiple PDAC cell models and effectively induces tumor regression without overt toxicity in PDAC cell line-derived xenograft and in more clinically relevant patient-derived xenograft models. Mechanistically, in addition to its canonical function of phosphorylating CDK1, PKMYT1 functions as an oncogene to promote PDAC tumorigenesis by regulating PLK1 expression and phosphorylation. Finally, TP53 function and PRKDC activation are shown to modulate the sensitivity to PKMYT1 inhibition. These results define PKMYT1 dependency in PDAC and identify potential therapeutic strategies for clinical translation.
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Affiliation(s)
- Simin Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yangjie Xiong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yuxiang Luo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yanying Shen
- Department of Pathology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Fengrui Zhang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, 200011, Shanghai, China
| | - Haoqi Lan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yuzhi Pang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaofang Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaoqi Li
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Xufen Zheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaojing Lu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaoxiao Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yumei Cheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Tanwen Wu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yue Dong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yuan Lu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, 200011, Shanghai, China
| | - Jiujie Cui
- Department of Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Xiaona Jia
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Sheng Yang
- Department of Oncology, Fujian Medical University Union Hospital, 350001, Fuzhou, Fujian, China
| | - Liwei Wang
- Department of Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Yuexiang Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.
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3
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Tomović Pavlović K, Kocić G, Šmelcerović A. Myt1 kinase inhibitors - Insight into structural features, offering potential frameworks. Chem Biol Interact 2024; 391:110901. [PMID: 38331334 DOI: 10.1016/j.cbi.2024.110901] [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: 11/27/2023] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
The cell cycle includes two checkpoint arrests allowing to repair of damaged DNA. Many cancer cell lines exhibit weak G1 checkpoint mechanisms relying significantly more on the G2 checkpoint than do healthy cells. Inhibition of Myt1 kinase (PKMYT1), a forgotten member of the Wee family, cyclin-dependent kinase 1 (Cdk1) inhibitory kinase, target for G2 checkpoint abrogation, whose inhibition forces cells into premature unchecked mitosis resulting in cell death, is a promising concept for anticancer therapy. There are not many inhibitors of this emerging, potentially clinically important kinase. Herein, the valuable insight into structural features and binding mechanisms of diaminopyrimidines, aminoquinolines, quinazolines, pyrido[2,3-d]pyrimidines, pyrazolo[3,4-d]pyrimidines, and pyrrolo[2,3-b]quinoxalines, as well as finally made a general scheme of fragmented structures of Myt1 inhibitors with the enzyme, offer potential frameworks useful for future directions, for further chemical optimizations, in the discovery and the design of novel effective structures, potential therapeutics.
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Affiliation(s)
- Katarina Tomović Pavlović
- Department of Pharmacy, Faculty of Medicine, University of Niš, Bulevar Dr Zorana Đinđića 81, 18000, Niš, Serbia.
| | - Gordana Kocić
- Department of Biochemistry, Faculty of Medicine, University of Niš, Bulevar Dr Zorana Đinđića 81, 18000, Niš, Serbia
| | - Andrija Šmelcerović
- Department of Chemistry, Faculty of Medicine, University of Niš, Bulevar Dr Zorana Đinđića 81, 18000, Niš, Serbia.
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Ren Q, Qu N, Sun J, Zhou J, Liu J, Ni L, Tong X, Zhang Z, Kong X, Wen Y, Wang Y, Wang D, Luo X, Zhang S, Zheng M, Li X. KinomeMETA: meta-learning enhanced kinome-wide polypharmacology profiling. Brief Bioinform 2023; 25:bbad461. [PMID: 38113075 PMCID: PMC10729787 DOI: 10.1093/bib/bbad461] [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: 08/27/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
Kinase inhibitors are crucial in cancer treatment, but drug resistance and side effects hinder the development of effective drugs. To address these challenges, it is essential to analyze the polypharmacology of kinase inhibitor and identify compound with high selectivity profile. This study presents KinomeMETA, a framework for profiling the activity of small molecule kinase inhibitors across a panel of 661 kinases. By training a meta-learner based on a graph neural network and fine-tuning it to create kinase-specific learners, KinomeMETA outperforms benchmark multi-task models and other kinase profiling models. It provides higher accuracy for understudied kinases with limited known data and broader coverage of kinase types, including important mutant kinases. Case studies on the discovery of new scaffold inhibitors for membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase and selective inhibitors for fibroblast growth factor receptors demonstrate the role of KinomeMETA in virtual screening and kinome-wide activity profiling. Overall, KinomeMETA has the potential to accelerate kinase drug discovery by more effectively exploring the kinase polypharmacology landscape.
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Affiliation(s)
- Qun Ren
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ning Qu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jingjing Sun
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jingyi Zhou
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Jin Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Ni
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xiaochu Tong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Zimei Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xiangtai Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yiming Wen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yitian Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Dingyan Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, Hangzhou 330106, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
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5
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Tamir TY, Drewry DH, Wells C, Major MB, Axtman AD. PKIS deep dive yields a chemical starting point for dark kinases and a cell active BRSK2 inhibitor. Sci Rep 2020; 10:15826. [PMID: 32985588 PMCID: PMC7522982 DOI: 10.1038/s41598-020-72869-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/08/2020] [Indexed: 01/14/2023] Open
Abstract
The Published Kinase Inhibitor Set (PKIS) is a publicly-available chemogenomic library distributed to more than 300 laboratories by GlaxoSmithKline (GSK) between 2011 and 2015 and by SGC-UNC from 2015 to 2017. Screening this library of well-annotated, published kinase inhibitors has yielded a plethora of data in diverse therapeutic and scientific areas, funded applications, publications, and provided impactful pre-clinical results. GW296115 is a compound that was included in PKIS based on its promising selectivity following profiling against 260 human kinases. Herein we present more comprehensive profiling data for 403 wild type human kinases and follow-up enzymatic screening results for GW296115. This more thorough investigation of GW296115 has confirmed it as a potent inhibitor of kinases including BRSK1 and BRSK2 that were identified in the original panel of 260 kinases as well as surfaced other kinases that it potently inhibits. Based on these new kinome-wide screening results, we report that GW296115 is an inhibitor of several members of the Illuminating the Druggable Genome (IDG) list of understudied dark kinases. Specifically, our results establish GW296115 as a potent lead chemical tool that inhibits six IDG kinases with IC50 values less than 100 nM. Focused studies establish that GW296115 is cell active, and directly engages BRSK2. Further evaluation showed that GW296115 downregulates BRSK2-driven phosphorylation and downstream signaling. Therefore, we present GW296115 as a cell-active chemical tool that can be used to interrogate the poorly characterized function(s) of BRSK2.
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Affiliation(s)
- Tigist Y Tamir
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Ben Major
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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6
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Zhang QY, Chen XQ, Liu XC, Wu DM. PKMYT1 Promotes Gastric Cancer Cell Proliferation and Apoptosis Resistance. Onco Targets Ther 2020; 13:7747-7757. [PMID: 32801781 PMCID: PMC7414979 DOI: 10.2147/ott.s255746] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/15/2020] [Indexed: 01/10/2023] Open
Abstract
Background Abnormal expression of protein kinase membrane associated tyrosine/threonine 1 (PKMYT1) is closely associated with multiple types of cancers. In the present study, we examined the roles of PKMYT1 in gastric cancer (GC) progression. Methods We examined the expression status of PKMYT1 in GC tissues and cell lines. Meanwhile, short hairpin RNA (shRNA) was used to inhibit the endogenous expression of PKMYT1 in GC cells. Then we analyzed the effect of PKMYT1 on the malignant biological behavior of GC cells by in vitro and in vivo experiments. Results The findings showed high PKMYT1 expressions in GC tissues as well as a positive correlation between PKMYT1 expression and prognosis of patients with GC. Additional findings also revealed that PKMYT1 silencing significantly enhanced apoptosis and inhibited GC cell proliferation. In vivo, the silence of PKMYT1 inhibits tumor growth. Further analysis showed that the increase in PKMYT1 expressions led to malignant biological behavior through activation of the MAPK signaling pathway. Conclusion Our data suggested that PKMYT1 promotes cell proliferation and apoptosis resistance in GC cells by activating the MAPK signaling pathway, making it a potential therapeutic target for GC.
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Affiliation(s)
- Qi-Yong Zhang
- Department of Gastroenterology, The First People's Hospital of Lanzhou, Lanzhou City, Gansu 730050, People's Republic of China
| | - Xiao-Qin Chen
- Department of Gastroenterology, The First People's Hospital of Lanzhou, Lanzhou City, Gansu 730050, People's Republic of China
| | - Xiong-Chang Liu
- Department of Gastroenterology, The First People's Hospital of Lanzhou, Lanzhou City, Gansu 730050, People's Republic of China
| | - De-Ming Wu
- Department of Gastroenterology, The First People's Hospital of Lanzhou, Lanzhou City, Gansu 730050, People's Republic of China
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7
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Gagic Z, Ruzic D, Djokovic N, Djikic T, Nikolic K. In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs. Front Chem 2020; 7:873. [PMID: 31970149 PMCID: PMC6960140 DOI: 10.3389/fchem.2019.00873] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Rational drug design implies usage of molecular modeling techniques such as pharmacophore modeling, molecular dynamics, virtual screening, and molecular docking to explain the activity of biomolecules, define molecular determinants for interaction with the drug target, and design more efficient drug candidates. Kinases play an essential role in cell function and therefore are extensively studied targets in drug design and discovery. Kinase inhibitors are clinically very important and widely used antineoplastic drugs. In this review, computational methods used in rational drug design of kinase inhibitors are discussed and compared, considering some representative case studies.
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Affiliation(s)
- Zarko Gagic
- Department of Pharmaceutical Chemistry, Faculty of Medicine, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Teodora Djikic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
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8
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Zhang Q, Zhao X, Zhang C, Wang W, Li F, Liu D, Wu K, Zhu D, Liu S, Shen C, Yuan X, Zhang K, Yang Y, Zhang Y, Zhao S. Overexpressed PKMYT1 promotes tumor progression and associates with poor survival in esophageal squamous cell carcinoma. Cancer Manag Res 2019; 11:7813-7824. [PMID: 31695486 PMCID: PMC6707438 DOI: 10.2147/cmar.s214243] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/25/2019] [Indexed: 12/29/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is one of the most common malignant tumors worldwide and the 5-year overall survival rate remains poor. Protein kinase, membrane associated tyrosine/threonine (PKMYT1) is overexpressed in several cancers and participate in tumor progression. However, the mechanism of PKMYT1 in ESCC is unclear. Purpose The objective of our study was to demonstrate the the expression and role of PKMYT1 in ESCC. Patients and methods We detected the expression of PKMYT1 in ESCC patients and analysed the correlation with overall survival time and disease-free survival time. Then we detected PKMYT1 expression in ESCC cell lines and immortalized human esophageal epithelial cell line. Down-regulated PKMYT1 was carried out in KYSE70 and KYSE450 cells to invetigate the mechanism of PKMYT1 in ESCC cells. Results PKMYT1 was up-regulated in tumor tissues and ESCC cell lines, and higher expression of PKMYT1 correlated with poorer overall survival in ESCC patients. Besides, in ESCC cell lines KYSE70 and KYSE450, knocking down PKMYT1 allowed more cells to skip G2/M checkpoint to complete mitosis, which promoted cell apoptosis, inhibited cell proliferation, and prevented the EMT phenotype in vitro. Meantime, we also observed that down-regulated PKMYT1 in ESCC cells suppressed AKT/mTOR signaling pathway. These results demonstrated PKMYT1 may act as an oncogene in ESCC. Conclusion PKMYT1 plays an crutial role in ESCC progression, downregulated PKMYT1 might inhibit the development of ESCC by AKT/mTOR signaling pathway, and might be a novel target in the treatment of ESCC.
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Affiliation(s)
- Qingyi Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province 450052, People's Republic of China
| | - Xuan Zhao
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China
| | - Chaoqi Zhang
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Wei Wang
- Henan Medical Association, Zhengzhou, Henan Province 450000, People's Republic of China
| | - Feng Li
- Department of Surgery, Competence Center of Thoracic Surgery, Charité University Hospital Berlin, Berlin 10117, Germany
| | - Donglei Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province 450052, People's Republic of China
| | - Kai Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province 450052, People's Republic of China
| | - Dengyan Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province 450052, People's Republic of China
| | - Shasha Liu
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China
| | - Chunyi Shen
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China
| | - Xin Yuan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Henan Province 450052, People's Republic of China
| | - Kai Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China
| | - Yang Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province 450052, People's Republic of China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China
| | - Song Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province 450052, People's Republic of China.,Key Laboratory of Thoracic Tumor of Zhengzhou City, Zhengzhou, Henan 450052, People's Republic of China
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9
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Wang XM, Li QY, Ren LL, Liu YM, Wang TS, Mu TC, Fu S, Liu C, Xiao JY. Effects of MCRS1 on proliferation, migration, invasion, and epithelial mesenchymal transition of gastric cancer cells by interacting with Pkmyt1 protein kinase. Cell Signal 2019; 59:171-181. [PMID: 30953699 DOI: 10.1016/j.cellsig.2019.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/31/2022]
Abstract
Microspherule protein 1(MCRS1) is known to be an oncogene in several tumors. However, recent studies have shown that MCRS1 inhibits lymphatic metastasis in gastric cancer (GC) patients by inhibiting telomerase activity. Protein kinase, membrane associated tyrosine/threonine 1(Pkmyt1), a member of the WEE1 family, has been found to interact with MCRS1 by yeast two-hybrid assay; however, how these two proteins interact in GC is still unclear. Hence, this study aimed to investigate the effect of MCRS1 interaction with Pkmyt1 on GC cell proliferation, migration, and invasion. Initially, we observed increased expression of MCRS1 in GC SGC-7901 cells and decreased expression in GC BGC-823 cells. Hence, we down-regulated MCRS1 expression in SGC-7901 cells and up-regulated it in BGC-823 cells. Our results showed that overexpression of MCRS1 inhibits the growth, invasion and migration of GC cells, while downregulation of MCRS1 promotes the growth, invasion and migration of GC cells. When MK1775, an inhibitor of WEE1 kinase, was added after downregulation of MCRS1, phenotypic recovery effects were observed. Overexpression of MCRS1 also inhibited the expression of Pkmyt1 and vice versa. This indicated that there might be a possible interaction between MCRS1 and Pkmyt1. Furthermore, immunoprecipitation assay revealed the interaction between MCRS1 and Pkmyt1 in virto, and immunofluorescence experiments showed that the two proteins were co-localized in the cytoplasm. In conclusion, our study confirmed the specific tumor suppressive activity of MCRS1 in GC proliferation, invasion and migration and suggested that it might inhibit the progression of GC through its interaction with Pkmyt1.
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Affiliation(s)
- Xin-Meng Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China.
| | - Qi-Yang Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China
| | - Li-Li Ren
- Department of Neurobiology, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China
| | - Yi-Meng Liu
- Department of Developmental Biology, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China
| | - Tian-Shi Wang
- Department of Food Science, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China
| | - Tian-Chi Mu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China
| | - Shuai Fu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China
| | - Chao Liu
- Department of Developmental Biology, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China.
| | - Jian-Ying Xiao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Jinzhou Medical University, 3 Songpo Road, Jinzhou, Liaoning Province 121000, PR China.
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10
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Najjar A, Platzer C, Luft A, Aßmann CA, Elghazawy NH, Erdmann F, Sippl W, Schmidt M. Computer-aided design, synthesis and biological characterization of novel inhibitors for PKMYT1. Eur J Med Chem 2018; 161:479-492. [PMID: 30388464 DOI: 10.1016/j.ejmech.2018.10.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/12/2022]
Abstract
In the current work, we applied computational methods to analyze the membrane-associated inhibitory kinase PKMYT1 and small molecule inhibitors. PKMYT1 regulates the cell cycle at G2/M transition and phosphorylates Thr14 and Tyr15 in the Cdk1-cyclin B complex. A combination of in silico and in vitro screening was applied to identify novel PKMYT1 inhibitors. The computational approach combined structural analysis, molecular docking, binding free energy calculations, and quantitative structure-activity relationship (QSAR) models. In addition, a computational fragment growing approach was applied to a set of previously identified diaminopyrimidines. Based on the derived computational models, several derivatives were synthesized and tested in vitro on PKMYT1. Novel inhibitors active in the sub-micromolar range were identified which provide the basis for further characterization of PKMYT1 as putative target for cancer therapy.
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Affiliation(s)
- Abdulkarim Najjar
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Charlott Platzer
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Anton Luft
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Chris Alexander Aßmann
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Nehal H Elghazawy
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Frank Erdmann
- Institute of Pharmacy, Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Matthias Schmidt
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany.
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