1
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Gao H, Zhang JY, Zhao LJ, Guo YY. Synthesis and clinical application of small-molecule inhibitors and PROTACs of anaplastic lymphoma kinase. Bioorg Chem 2023; 140:106807. [PMID: 37651895 DOI: 10.1016/j.bioorg.2023.106807] [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: 06/12/2023] [Revised: 07/13/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
Pharmacological interventions that specifically target protein products of oncogenes in tumors have surfaced as a propitious therapeutic approach. Among infrequent genetic alterations, rearrangements of the anaplastic lymphoma kinase (ALK) gene, typically involving a chromosome 2 inversion that culminates in a fusion with the echinoderm microtubule-associated protein like 4 (EML4), lead to anomalous expression and activation of ALK. The inhibition of autophosphorylation and subsequent blockade of signal transduction by ALK tyrosine kinase inhibitors (TKIs) has been observed to elicit anti-tumor effects. Currently, four generations of ALK-positive targeted drugs have been investigated, providing a promising outlook for patients. The aim of this review is to furnish a comprehensive survey of the synthesis and clinical application of prototypical small-molecule ALK inhibitors in both preclinical and clinical phases, offering guidance for further development of ALK inhibitors for cancer therapy.
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Affiliation(s)
- Hua Gao
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jing-Yi Zhang
- The Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States; College of Chemistry and Chemical Engineering, Zhengzhou Normal University 450044, China.
| | - Li-Jie Zhao
- The Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States.
| | - Yuan-Yuan Guo
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China.
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2
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Cui Y, Tan Z, Liu S, Cao Z, Shao B, Guo M, Jiang N, Zhai X. Fragment-based discovery of novel phenyltriazolyl derivatives as allosteric type-I 1/2 ALK inhibitors with promising antitumor effects. Bioorg Med Chem Lett 2022; 75:128990. [PMID: 36113668 DOI: 10.1016/j.bmcl.2022.128990] [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: 07/21/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022]
Abstract
Based on the high-throughput screening hit BY-1, a series of phenyltriazolyl derivatives were developed. Satisfyingly, most compounds were detected moderate to excellent antitumor effects against Karpas299 and H2228 cells. Among them, 12k bearing 4‑hydroxypiperidinyl group exhibited the optimal activities against tested cells with IC50 values of 51 nM and 175 nM, as well as promising inhibitory effects on ALKWT (3.7 nM) and ALKL1196M (6.8 nM). Unlike the conventional type-I ALK inhibitors, molecular models identified 12k as an allosteric type-I1/2 inhibitor by forming key interactions in both the ATP binding region and the hydrophobic back pocket of ALK. Intriguingly, 12k could dose-dependently induce apoptosis on H2228 cell and inhibit colony formation and tumor cell migration. Taken together, the rationalization of 12k may shed new light on the identification of novel allosteric type-I1/2 ALK inhibitors.
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Affiliation(s)
- Youbao Cui
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zehui Tan
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shuyu Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhi Cao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Bin Shao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengrao Guo
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Nan Jiang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
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3
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Jiang GL, Song LH, Qiu YF, Liu Y. 3D-QSAR and Docking Studies on Pyrimidine Derivatives of Second-Generation ALK Inhibitors. PHARMACEUTICAL FRONTS 2022. [DOI: 10.1055/s-0042-1750044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
AbstractAnaplastic lymphoma kinase (ALK) is a promising target for the treatment of non-small cell lung cancer. Under crizotinib treatment, drug resistance and progressive disease appeared after the point mutations arising in the kinase domain of ALK. Second-generation ALK inhibitors can solve the deficiencies of the first generation, especially the drug resistance in cancer chemotherapy. Ceritinib (LDK378), a pyrimidine derivative, for example, can inhibit the activity of ALK with an IC50 value of 40.7 nmol/L, and can experience disease progression after initial treatment with crizotinib. Unfortunately, clear structure–activity relationships have not been identified to date, impeding the rational design of future compounds possessing ALK inhibition activity. To explore interesting insights into the structures of pyrimidine derivatives that influence the activities of the second-generation ALK inhibitors, three-dimensional quantitative structure–activity relationship (3D-QSAR) and molecular docking were performed on a total of 45 derivatives of pyrimidine. Comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) techniques were used to generate 3D-QSAR models. CoMFA and CoMSIA were performed using the Sybyl X 2.0 package. Molecular docking analysis was performed using the Surflex-Dock module in SYBYL-X 2.0 package. We found in the CoMFA model that the non-cross-validated r2
value was 0.998, the cross-validated q
2 value was 0.663, and the F statistic value was 2,401.970, while the r2
value was 0.988; q
2 value was 0.730, and F value was 542.933 in CoMSIA models, suggesting the good predictability of the CoMFA and CoMSIA models. 3D contour maps and docking results suggested that different groups on the core parts of the compounds could enhance the biological activities. Based on these results, the established 3D-QSAR models and the binding structures of ALK inhibitors obtained favor the prediction of the activity of new inhibitors and will be helpful in the reasonable design of ALK inhibitors in the future.
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Affiliation(s)
- Gang-Long Jiang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State institute of Pharmaceutical Industry, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Lian-Hua Song
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Yong-Fu Qiu
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State institute of Pharmaceutical Industry, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Yu Liu
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State institute of Pharmaceutical Industry, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State institute of Pharmaceutical Industry, Shanghai, People's Republic of China
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4
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Brenner AK, Gunnes MW. Therapeutic Targeting of the Anaplastic Lymphoma Kinase (ALK) in Neuroblastoma-A Comprehensive Update. Pharmaceutics 2021; 13:pharmaceutics13091427. [PMID: 34575503 PMCID: PMC8470592 DOI: 10.3390/pharmaceutics13091427] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 01/27/2023] Open
Abstract
Neuroblastoma (NBL) is an embryonic malignancy of the sympathetic nervous system and mostly affects children under the age of five. NBL is highly heterogeneous and ranges from spontaneously regressing to highly aggressive disease. One of the risk factors for poor prognosis are aberrations in the receptor tyrosine kinase anaplastic lymphoma kinase (ALK), which is involved in the normal development and function of the nervous system. ALK mutations lead to constitutive activation of ALK and its downstream signalling pathways, thus driving tumorigenesis. A wide range of steric ALK inhibitors has been synthesized, and several of these inhibitors are already in clinical use. Major challenges are acquired drug resistance to steric inhibitors and pathway evasion strategies of cancer cells upon targeted therapy. This review will give a comprehensive overview on ALK inhibitors in clinical use in high-risk NBL and on the potential and limitations of novel inhibitors. Because combinatory treatment regimens are probably less likely to induce drug resistance, a special focus will be on the combination of ALK inhibitors with drugs that either target downstream signalling pathways or that affect the survival and proliferation of cancer cells in general.
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5
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Li Z, Liu F, Wu S, Ding S, Chen Y, Liu J. Research progress on the drug resistance of ALK kinase inhibitors. Curr Med Chem 2021; 29:2456-2475. [PMID: 34365942 DOI: 10.2174/0929867328666210806120347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The fusion and rearrangement of the ALK gene of anaplastic lymphoma kinase is an important cause of a variety of cancers, including non-small cell lung cancer (NSCLC) and anaplastic large cell lymphoma (ALCL). Since crizotinib first came out, many ALK inhibitors have come out one after another, but the fatal flaw in each generation of ALK inhibitors is the body's resistance to drugs. Therefore, how to solve the problem of drug resistance has become an important bottleneck in the application and development of ALK inhibitors. This article briefly introduces the drug resistance of ALK inhibitors and the modified forms of ALK inhibitors, which provide a theoretical basis for solving the drug resistance of ALK inhibitors and the development of a new generation of ALK kinase inhibitors. METHOD We use relevant databases to query relevant literature, and then screen and select based on the relevance and cutting edge of the content. We then summarize and analyze appropriate articles, integrate and classify relevant studies, and finally write articles based on topics. RESULT This article starts with the problem of ALK resistance, first introduces the composition of ALK kinase, and then introduces the problem of resistance of ALK kinase inhibitors. Later, the structural modification to overcome ALK resistance was introduced, and finally, the method to overcome ALK resistance was introduced. CONCLUSION This article summarizes the resistance pathways of ALK kinase inhibitors, and integrates the efforts made to overcome the structural modification of ALK resistance problems, and hopes to provide some inspiration for the development of the next generation of ALK kinase inhibitors.
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Affiliation(s)
- Zhen Li
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Fang Liu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Shuang Wu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Shi Ding
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Ye Chen
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Ju Liu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
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6
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Iżykowska K, Rassek K, Korsak D, Przybylski GK. Novel targeted therapies of T cell lymphomas. J Hematol Oncol 2020; 13:176. [PMID: 33384022 PMCID: PMC7775630 DOI: 10.1186/s13045-020-01006-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/22/2020] [Indexed: 02/06/2023] Open
Abstract
T cell lymphomas (TCL) comprise a heterogeneous group of non-Hodgkin lymphomas (NHL) that often present at an advanced stage at the time of diagnosis and that most commonly have an aggressive clinical course. Treatment in the front-line setting is most often cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) or CHOP-like regimens, which are effective in B cell lymphomas, but in TCL are associated with a high failure rate and frequent relapses. Furthermore, in contrast to B cell NHL, in which substantial clinical progress has been made with the introduction of monoclonal antibodies, no comparable advances have been seen in TCL. To change this situation and improve the prognosis in TCL, new gene-targeted therapies must be developed. This is now possible due to enormous progress that has been made in the last years in the understanding of the biology and molecular pathogenesis of TCL, which enables the implementation of the research findings in clinical practice. In this review, we present new therapies and current clinical and preclinical trials on targeted treatments for TCL using histone deacetylase inhibitors (HDACi), antibodies, chimeric antigen receptor T cells (CARTs), phosphatidylinositol 3-kinase inhibitors (PI3Ki), anaplastic lymphoma kinase inhibitors (ALKi), and antibiotics, used alone or in combinations. The recent clinical success of ALKi and conjugated anti-CD30 antibody (brentuximab-vedotin) suggests that novel therapies for TCL can significantly improve outcomes when properly targeted.
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Affiliation(s)
- Katarzyna Iżykowska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Karolina Rassek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Dorota Korsak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Grzegorz K Przybylski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland.
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7
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Chen J, Wang W, Sun H, Pang L, Yin B. Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics. J Comput Aided Mol Des 2020; 34:1289-1305. [DOI: 10.1007/s10822-020-00355-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022]
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8
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Design, synthesis and biological evaluation of 2-arylaminopyrimidine derivatives bearing 1,3,8-triazaspiro[4,5]decan-4-one or piperidine-3-carboxamide moiety as novel Type-I1/2 ALK inhibitors. Bioorg Chem 2020; 94:103456. [DOI: 10.1016/j.bioorg.2019.103456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/05/2019] [Accepted: 11/19/2019] [Indexed: 11/19/2022]
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9
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Liu S, Jiang Y, Yan R, Li Z, Wan S, Zhang T, Wu X, Hou J, Zhu Z, Tian Y, Zhang J. Design, synthesis and biological evaluations of 2-amino-4-(1-piperidine) pyridine derivatives as novel anti crizotinib-resistant ALK/ROS1 dual inhibitors. Eur J Med Chem 2019; 179:358-375. [PMID: 31260890 DOI: 10.1016/j.ejmech.2019.06.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/29/2019] [Accepted: 06/15/2019] [Indexed: 12/11/2022]
Abstract
ALK and ROS1 kinases have become promising therapeutic targets since Crizotinib was used to treat non-small-cell lung cancer clinically. Aiming to explore new potent inhibitors, a series of 2-amino-4-(1-piperidine) pyridine derivatives that stabilized a novel DFG-shifted conformation in the kinase domain of ALK were designed and synthesized on the base of lead compound A. Biological evaluation highlighted that most of these new compounds could also potently inhibit ROS1 kinase, leading to the promising inhibitors against both ROS1 and ALK. Among them, the representative compound 2e stood out potent anti-proliferative activity against ALK-addicted H3122 and ROS1-addicted HCC78 cell lines (IC50 = 6.27 μM and 10.71 μM, respectively), which were comparable to that of Crizotinib. Moreover, 2e showed impressive enzyme activity against clinically Crizotinib-resistant ALKL1196M with an IC50 value of 41.3 nM, which was about 2-fold more potent than that of Crizotinib. 2e also showed potent inhibitory activity in about 6-fold superior to Crizotinib (IC50: 104.7 nM vs. 643.5 nM) in Ba/F3 cell line harboring ROS1G2032R. Furthermore, molecular modeling disclosed that all the representative inhibitors could dock into the active site of ALK and ROS1, which gave a probable explanation of anti Crizotinib-resistant mutants. These results indicated that our work has established a path forward for the generation of anti Crizotinib-resistant ALK/ROS1 dual inhibitors.
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Affiliation(s)
- Siming Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ying Jiang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ruohong Yan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhonghuang Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Tingting Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Xiaoyun Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ju Hou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhengguang Zhu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China.
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China.
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10
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Li JY, Chen HY, Dai WJ, Lv QJ, Chen CYC. Artificial Intelligence Approach To Investigate the Longevity Drug. J Phys Chem Lett 2019; 10:4947-4961. [PMID: 31411476 DOI: 10.1021/acs.jpclett.9b02220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Longevity is a very important and interesting topic, and Klotho has been demonstrated to be related to longevity. We combined network pharmacology, machine learning, deep learning, and molecular dynamics (MD) simulation to investigate potent lead drugs. Related protein insulin-like growth factor 1 receptor (IGF1R) and insulin receptor (IR) were docked with the traditional Chinese medicine (TCM) database to screen out several novel candidates. Besides, nine different machine learning algorithms were performed to build reliable and accurate predicted models. Moreover, we used the novel deep learning algorithm to build predicted models. All of these models obtained significant R2, which are all greater than 0.87 on the training set and higher than 0.88 for the test set, respectively. The long time 500 ns molecular dynamics simulation was also performed to verify protein-ligand properties and stability. Finally, we obtained Antifebrile Dichroa, Holarrhena antidysenterica, and Gelsemium sempervirens, which might be potent TCMs for two targets.
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Affiliation(s)
- Jun-Yan Li
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center, Sun Yat-sen University, Shenzhen 510275, China
| | - Hsin-Yi Chen
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center, Sun Yat-sen University, Shenzhen 510275, China
| | - Wen-Jie Dai
- School of Pharmacy, Sun Yat-sen University, Shenzhen 510275, China
| | - Qiu-Jie Lv
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center, Sun Yat-sen University, Shenzhen 510275, China
| | - Calvin Yu-Chian Chen
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center, Sun Yat-sen University, Shenzhen 510275, China
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
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11
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Kong X, Pan P, Sun H, Xia H, Wang X, Li Y, Hou T. Drug Discovery Targeting Anaplastic Lymphoma Kinase (ALK). J Med Chem 2019; 62:10927-10954. [PMID: 31419130 DOI: 10.1021/acs.jmedchem.9b00446] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As a receptor tyrosine kinase of insulin receptor (IR) subfamily, anaplastic lymphoma kinase (ALK) has been validated to play important roles in various cancers, especially anaplastic large cell lymphoma (ALCL), nonsmall cell lung cancer (NSCLC), and neuroblastomas. Currently, five small-molecule inhibitors of ALK, including Crizotinib, Ceritinib, Alectinib, Brigatinib, and Lorlatinib, have been approved by the U.S. Food and Drug Administration (FDA) against ALK-positive NSCLCs. Novel type-I1/2 and type-II ALK inhibitors with improved kinase selectivity and enhanced capability to combat drug resistance have also been reported. Moreover, the "proteolysis targeting chimera" (PROTAC) technique has been successfully applied in developing ALK degraders, which opened a new avenue for targeted ALK therapies. This review provides an overview of the physiological and biological functions of ALK, the discovery and development of drugs targeting ALK by focusing on their chemotypes, activity, selectivity, and resistance as well as potential therapeutic strategies to overcome drug resistance.
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Affiliation(s)
- Xiaotian Kong
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China.,Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Peichen Pan
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Hongguang Xia
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital , Zhejiang University , Hangzhou 310058 , China
| | - Xuwen Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
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12
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Kong X, Sun H, Pan P, Zhu F, Chang S, Xu L, Li Y, Hou T. Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK. Phys Chem Chem Phys 2018; 20:4851-4863. [DOI: 10.1039/c7cp08241j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Anaplastic lymphoma kinase (ALK) has been regarded as a promising target for the therapy of various cancers.
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Affiliation(s)
- Xiaotian Kong
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
- Institute of Functional Nano and Soft Materials (FUNSOM)
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Feng Zhu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
- Institute of Functional Nano and Soft Materials (FUNSOM)
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13
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Pan P, Yu H, Liu Q, Kong X, Chen H, Chen J, Liu Q, Li D, Kang Y, Sun H, Zhou W, Tian S, Cui S, Zhu F, Li Y, Huang Y, Hou T. Combating Drug-Resistant Mutants of Anaplastic Lymphoma Kinase with Potent and Selective Type-I 1/2 Inhibitors by Stabilizing Unique DFG-Shifted Loop Conformation. ACS CENTRAL SCIENCE 2017; 3:1208-1220. [PMID: 29202023 PMCID: PMC5704298 DOI: 10.1021/acscentsci.7b00419] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Indexed: 05/07/2023]
Abstract
Targeted inhibition of anaplastic lymphoma kinase (ALK) dramatically improved therapeutic outcomes in the treatment of ALK-positive cancers, but unfortunately patients invariably progressed due to acquired resistance mutations in ALK. Currently available drugs are all type-I inhibitors bound to the ATP-binding pocket and are most likely to be resistant in patients harboring genetic mutations surrounding the ATP pocket. To overcome drug resistance, we rationally designed a novel kind of "bridge" inhibitor, which specially bind into an extended hydrophobic back pocket adjacent to the ATP-binding site of ALK. The novel type-I1/2 inhibitors display excellent antiproliferation activity against ALK-positive cancer cells and appear superior to two clinically used drugs, crizotinib and ceritinib. Structural and molecular modeling analyses indicate that the inhibitor induces dramatic conformational transition and stabilizes unique DFG-shifted loop conformation, enabling persistent sensitivity to different genetic mutations in ALK. These data highlight a rationale for further development of next-generation ALK inhibitors to combat drug resistance.
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Affiliation(s)
- Peichen Pan
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huidong Yu
- Rongene
Pharma Co., Ltd., Shenzhen, Guandong 518054, China
| | - Qinglan Liu
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
- Innovative
Drug R & D Center, Shenzhen Salubris
Pharmaceuticals Co., Ltd., Huabao Industrial Zone, Shenzhen 518102, China
| | - Xiaotian Kong
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Institute of Functional Nano and
Soft Materials (FUNSOM) and Jiangsu Key Laboratory
of Translational Research and Therapy for Neuropsychiatric Diseases
and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hu Chen
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Jiean Chen
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Qi Liu
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Dan Li
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wenfang Zhou
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sheng Tian
- Institute of Functional Nano and
Soft Materials (FUNSOM) and Jiangsu Key Laboratory
of Translational Research and Therapy for Neuropsychiatric Diseases
and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Sunliang Cui
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Youyong Li
- Institute of Functional Nano and
Soft Materials (FUNSOM) and Jiangsu Key Laboratory
of Translational Research and Therapy for Neuropsychiatric Diseases
and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yong Huang
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
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14
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Shin S, Mah S, Hong S, Park H. Discovery of Low Micromolar Dual Inhibitors for Wild Type and L1196M Mutant of Anaplastic Lymphoma Kinase through Structure-Based Virtual Screening. J Chem Inf Model 2016; 56:802-10. [PMID: 27014917 DOI: 10.1021/acs.jcim.6b00026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although anaplastic lymphoma kinase (ALK) is involved in a variety of malignant human cancers, the emergence of constitutively active mutants with drug resistance has rendered it difficult to identify the new medicines for ALK-dependent cancers. To find the common inhibitors of the wild type ALK and the most abundant drug-resistant mutant (L1196M), we performed molecular docking-based virtual screening of a large chemical library in parallel for the two target proteins. As a consequence of augmenting the accuracy of the docking simulation by implementing a sophisticated hydration free energy term in the scoring function, 12 common inhibitors are discovered with the inhibitory activities ranging from submicromolar to low micromolar levels. The results of the binding free energy decomposition indicate that the biochemical potency of ALK inhibitors can be optimized by reducing the dehydration cost for binding to the receptor protein as well as by strengthening the interactions with amino acid residues in the ATP-binding site. The newly identified ALK inhibitors are found to have a little higher inhibitory activity for the L1196M mutant than for the wild type due to the strengthening of the hydrogen bond interactions in the ATP-binding site. Of the 12 common inhibitors, 2-(5-methyl-benzooxazol-2-ylamino)-quinazolin-4-ol (3) is anticipated to serve as a new molecular scaffold to optimize the biochemical potency because it exhibits low micromolar inhibitory activity with respect to both the wild type and L1196M mutant in spite of the low molecular weight (292.3 amu).
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Affiliation(s)
- Saemina Shin
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University , 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea
| | - Shinmee Mah
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) & Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 305-701, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) & Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 305-701, Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University , 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea
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15
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Design, Synthesis, and Evaluation of 2-Anilino-4-(3,5-dicarboxamidespiperidine)-pyrimidines as Anaplastic Lymphoma Kinase Inhibitors. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Puig de la Bellacasa R, Karachaliou N, Estrada-Tejedor R, Teixidó J, Costa C, Borrell JI. ALK and ROS1 as a joint target for the treatment of lung cancer: a review. Transl Lung Cancer Res 2015; 2:72-86. [PMID: 25806218 DOI: 10.3978/j.issn.2218-6751.2013.03.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/25/2013] [Indexed: 12/14/2022]
Abstract
Rearrangements of the anaplastic lymphoma kinase (ALK) have been described in multiple malignancies, including non-small cell lung cancer (NSCLC). ALK fusions have gain of function properties while activating mutations in wild-type ALK can also occur within the tyrosine kinase domain. ALK rearrangements define a new molecular subtype of NSCLC that is exquisitely sensitive to ALK inhibition. Crizotinib, an orally available small molecule ATP-mimetic compound which was originally designed as a MET inhibitor, was recognized to have "off-target" anti-ALK activity and has been approved in the USA for the treatment of patients with ALK-positive NSCLC. Chromosomal rearrangements involving the ROS1 receptor tyrosine kinase have also been recently described in NSCLC, while crizotinib is currently under clinical trial in this molecular subset of NSCLC patients. The basic approaches of any computer aided drug design work in terms of structure and ligand based drug design. Details of each of these approaches should be covered with an emphasis on utilizing both in order to develop multi-targeted small-molecule kinase inhibitors. Such multi-targeted tyrosine kinase inhibitors can have antiproliferative activity against both ROS1and ALK rearranged NSCLC. Herein, we highlight the importance of targeting these proteins and the advances in optimizing more potent and selective ALK and ROS1 kinase inhibitors.
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Affiliation(s)
- Raimon Puig de la Bellacasa
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Niki Karachaliou
- Breakthrough Cancer Research Unit, Pangaea Biotech S.L, Barcelona, Spain
| | - Roger Estrada-Tejedor
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Jordi Teixidó
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Carlota Costa
- Breakthrough Cancer Research Unit, Pangaea Biotech S.L, Barcelona, Spain
| | - José I Borrell
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
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17
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Ai X, Shen S, Shen L, Lu S. An interaction map of small-molecule kinase inhibitors with anaplastic lymphoma kinase (ALK) mutants in ALK-positive non-small cell lung cancer. Biochimie 2015; 112:111-20. [PMID: 25769414 DOI: 10.1016/j.biochi.2015.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/02/2015] [Indexed: 12/16/2022]
Abstract
Human anaplastic lymphoma kinase (ALK) has become a well-established target for the treatment of ALK-positive non-small cell lung cancer (NSCLC). Here, we have profiled seven small-molecule inhibitors, including 2 that are approved drugs, against a panel of clinically relevant mutations in ALK tyrosine kinase (TK) domain, aiming at a comprehensive understanding of molecular mechanism and biological implication underlying inhibitor response to ALK TK mutation. We find that (i) the gatekeeper mutation L1196M causes crizotinib resistance by simultaneously increasing and decreasing the binding affinities of, respectively, ATP and inhibitor to ALK, whereas the secondary mutation C1156Y, which is located far away from the ATP-binding site of ALK TK domain, causes the resistance by inducing marked allosteric effect on the site, (ii) the 2nd and 3rd generation kinase inhibitors exhibit relatively high sensitivity towards ALK mutants as compared to 1st generation inhibitors, (iii) the pan-kinase inhibitor staurosporine is insensitive for most mutations due to its high structural compatibility, and (iv) ATP affinity to ALK is generally reduced upon most clinically relevant mutations. Furthermore, we also identify six novel mutation-inhibitor pairs that are potentially associated with drug resistance. In addition, the G1202R and C1156Y mutations are expected to generally cause resistance for many existing inhibitors, since they can address significant effect on the geometric shape and physicochemical property of ALK active pocket.
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Affiliation(s)
- Xinghao Ai
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shengping Shen
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lan Shen
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shun Lu
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China.
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18
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Kong X, Pan P, Li D, Tian S, Li Y, Hou T. Importance of protein flexibility in ranking inhibitor affinities: modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors. Phys Chem Chem Phys 2015; 17:6098-113. [DOI: 10.1039/c4cp05440g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Anaplastic lymphoma kinase (ALK) has gained increased attention as an attractive therapeutic target for the treatment of various cancers, especially non-small-cell lung cancer (NSCLC).
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Affiliation(s)
- Xiaotian Kong
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
- College of Pharmaceutical Sciences
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19
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Mesaros EF, Ott GR, Dorsey BD. Anaplastic lymphoma kinase inhibitors as anticancer therapeutics: a patent review. Expert Opin Ther Pat 2014; 24:417-42. [DOI: 10.1517/13543776.2014.877890] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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20
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Ortiz GX, Kang B, Wang Q. One-Pot Synthesis of 3-Azido- and 3-Aminopiperidines by Intramolecular Cyclization of Unsaturated Amines. J Org Chem 2014; 79:571-81. [DOI: 10.1021/jo4022666] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Gerardo X. Ortiz
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Bora Kang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Qiu Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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21
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Sun H, Li Y, Shen M, Tian S, Xu L, Pan P, Guan Y, Hou T. Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. Phys Chem Chem Phys 2014; 16:22035-45. [DOI: 10.1039/c4cp03179b] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We have thoroughly investigated the performance of MM/GBSA and MM/PBSA methodologies on virtual screening based on various protocols for kinase targets.
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Affiliation(s)
- Huiyong Sun
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
- College of Pharmaceutical Sciences
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
| | - Mingyun Shen
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
| | - Lei Xu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou, P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou, P. R. China
| | - Yan Guan
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
- College of Pharmaceutical Sciences
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22
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23
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Rosenbaum L, Dörr A, Bauer MR, Boeckler FM, Zell A. Inferring multi-target QSAR models with taxonomy-based multi-task learning. J Cheminform 2013; 5:33. [PMID: 23842210 PMCID: PMC4104930 DOI: 10.1186/1758-2946-5-33] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/03/2013] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND A plethora of studies indicate that the development of multi-target drugs is beneficial for complex diseases like cancer. Accurate QSAR models for each of the desired targets assist the optimization of a lead candidate by the prediction of affinity profiles. Often, the targets of a multi-target drug are sufficiently similar such that, in principle, knowledge can be transferred between the QSAR models to improve the model accuracy. In this study, we present two different multi-task algorithms from the field of transfer learning that can exploit the similarity between several targets to transfer knowledge between the target specific QSAR models. RESULTS We evaluated the two methods on simulated data and a data set of 112 human kinases assembled from the public database ChEMBL. The relatedness between the kinase targets was derived from the taxonomy of the humane kinome. The experiments show that multi-task learning increases the performance compared to training separate models on both types of data given a sufficient similarity between the tasks. On the kinase data, the best multi-task approach improved the mean squared error of the QSAR models of 58 kinase targets. CONCLUSIONS Multi-task learning is a valuable approach for inferring multi-target QSAR models for lead optimization. The application of multi-task learning is most beneficial if knowledge can be transferred from a similar task with a lot of in-domain knowledge to a task with little in-domain knowledge. Furthermore, the benefit increases with a decreasing overlap between the chemical space spanned by the tasks.
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Affiliation(s)
- Lars Rosenbaum
- Center for Bioinformatics (ZBIT), University of Tübingen, Sand 1,
Tübingen 72076, Germany
| | - Alexander Dörr
- Center for Bioinformatics (ZBIT), University of Tübingen, Sand 1,
Tübingen 72076, Germany
| | - Matthias R Bauer
- Institute of Pharmaceutical Sciences, University of Tübingen, Auf der
Morgenstelle 8, Tübingen 72076, Germany
| | - Frank M Boeckler
- Institute of Pharmaceutical Sciences, University of Tübingen, Auf der
Morgenstelle 8, Tübingen 72076, Germany
| | - Andreas Zell
- Center for Bioinformatics (ZBIT), University of Tübingen, Sand 1,
Tübingen 72076, Germany
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24
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Design of novel anaplastic lymphoma kinase (ALK) inhibitors based on predictive 3D QSAR models using different alignment strategies. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0662-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Benzyl 3-deoxy-3-(3,4,5-trimethoxybenzylamino)-β-L-xylopyranoside. MOLBANK 2013. [DOI: 10.3390/m793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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26
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Epstein LF, Chen H, Emkey R, Whittington DA. The R1275Q neuroblastoma mutant and certain ATP-competitive inhibitors stabilize alternative activation loop conformations of anaplastic lymphoma kinase. J Biol Chem 2012; 287:37447-57. [PMID: 22932897 DOI: 10.1074/jbc.m112.391425] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that, when genetically altered by mutation, amplification, chromosomal translocation or inversion, has been shown to play an oncogenic role in certain cancers. Small molecule inhibitors targeting the kinase activity of ALK have proven to be effective therapies in certain ALK-driven malignancies and one such inhibitor, crizotinib, is now approved for the treatment of EML4-ALK-driven, non-small cell lung cancer. In neuroblastoma, activating point mutations in the ALK kinase domain can drive disease progression, with the two most common mutations being F1174L and R1275Q. We report here crystal structures of the ALK kinase domain containing the F1174L and R1275Q mutations. Also included are crystal structures of ALK in complex with novel small molecule ALK inhibitors, including a classic type II inhibitor, that stabilize previously unobserved conformations of the ALK activation loop. Collectively, these structures illustrate a different series of activation loop conformations than has been observed in previous ALK crystal structures and provide insight into the activating nature of the R1275Q mutation. The novel active site topologies presented here may also aid the structure-based drug design of a new generation of ALK inhibitors.
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Affiliation(s)
- Linda F Epstein
- Department of Molecular Structure and Characterization, Amgen Inc., Cambridge, Massachusetts 02142, USA
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