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Combarel D, Dousset L, Bouchet S, Ferrer F, Tetu P, Lebbe C, Ciccolini J, Meyer N, Paci A. Tyrosine kinase inhibitors in cancers: Treatment optimization - Part I. Crit Rev Oncol Hematol 2024; 199:104384. [PMID: 38762217 DOI: 10.1016/j.critrevonc.2024.104384] [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: 01/24/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
A multitude of TKI has been developed and approved targeting various oncogenetic alterations. While these have provided improvements in efficacy compared with conventional chemotherapies, resistance to targeted therapies occurs. Mutations in the kinase domain result in the inability of TKI to inactivate the protein kinase. Also, gene amplification, increased protein expression and downstream activation or bypassing of signalling pathways are commonly reported mechanisms of resistance. Improved understanding of mechanisms involved in TKI resistance has resulted in the development of new generations of targeted agents. In a race against time, the search for new, more potent and efficient drugs, and/or combinations of drugs, remains necessary as new resistance mechanisms to the latest generation of TKI emerge. This review examines the various generations of TKI approved to date and their common mechanisms of resistance, focusing on TKI targeting BCR-ABL, epidermal growth factor receptor, anaplastic lymphoma kinase and BRAF/MEK tyrosine kinases.
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Affiliation(s)
- David Combarel
- Service de Pharmacologie, Département de Biologie et Pathologie médicales, Gustave Roussy, Villejuif 94805, France; Service de Pharmacocinétique, Faculté de Pharmacie, Université Paris Saclay, Châtenay-Malabry 92 296, France
| | - Léa Dousset
- Dermatology Department, Bordeaux University Hospital, Bordeaux, France
| | - Stéphane Bouchet
- Département de Pharmacologie, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Florent Ferrer
- Department of Pharmacology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France; SMARTc Unit, CRCM Inserm U1068, Aix Marseille Univ and APHM, Marseille, France
| | - Pauline Tetu
- Department of Dermatology, APHP Dermatology, Paris 7 Diderot University, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Céleste Lebbe
- Department of Dermatology, APHP Dermatology, Paris 7 Diderot University, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Joseph Ciccolini
- SMARTc Unit, CRCM Inserm U1068, Aix Marseille Univ and APHM, Marseille, France
| | - Nicolas Meyer
- Université Paul Sabatier-Toulouse III, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1037-CRCT, Toulouse, France
| | - Angelo Paci
- Service de Pharmacologie, Département de Biologie et Pathologie médicales, Gustave Roussy, Villejuif 94805, France; Service de Pharmacocinétique, Faculté de Pharmacie, Université Paris Saclay, Châtenay-Malabry 92 296, France.
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Chen Q, Zhang J, Wang X, Zong W, Sun L, Qin J, Yin Y. Two case reports: EML4-ALK rearrangement large cell neuroendocrine carcinoma and literature review. Front Oncol 2023; 13:1227980. [PMID: 38023218 PMCID: PMC10646488 DOI: 10.3389/fonc.2023.1227980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Anaplastic lymphoma kinase gene (ALK) rearrangement is present in only approximately 5% of non-small cell lung cancers (NSCLCs) and is scarce in LCNEC patients. The conventional first-line treatment options are chemotherapy combined with immunotherapy or chemotherapy followed by palliative radiotherapy. In this report, we present two cases of metastatic LCNEC with EML4-ALK fusion that were treated with ALK-TKI inhibitors and demonstrated a rapid therapeutic response. Both patients were nonsmoking women who declined cytotoxic chemotherapy, underwent Next-Generation Sequencing (NGS), and confirmed EML4-ALK fusion. They were treated with alectinib as first-line therapy, and the tumors showed significant shrinkage after two months, achieving a PR (defined as a more than 30% decrease in the sum of maximal dimensions). The PFS was 22 months and 32 months, respectively, until the last follow-up. A systematic review of all previously reported cases of LCNEC with ALK mutations identified only 21 cases. These cases were characterized by being female (71.4%), nonsmoking (85.7%), diagnosed at a relatively young age (median age 51.1), and stage IV (89.5%), with an overall response rate (ORR) of 90.5%. PFS and OS were significantly longer than those treated with conventional chemotherapy/immunotherapy. Based on the clinical characteristics and the effective therapeutic outcomes with ALK inhibitors in LCNEC patients with ALK fusion, we recommend routine ALK IHC (economical, affordable, and convenient, but with higher false positives) as a screening method in advanced LCNEC patients, particularly nonsmoking females or those who are not candidates for or unwilling to undergo cytotoxic chemotherapy. Further molecular profiling is necessary to confirm these potential beneficiaries. We suggest TKI inhibitors as the first-line treatment for metastatic LCNEC with ALK fusion. Additional studies on larger cohorts are required to assess the prevalence of ALK gene fusions and their sensitivity to various ALK inhibitors.
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Affiliation(s)
- Qin Chen
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, China
| | - Jingjing Zhang
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, China
| | - Xuan Wang
- Department of Neurosurgery, Tianjin, China
| | - Wenkang Zong
- Department of Pathology, Tianjin Chest Hospital, Tianjin, China
| | - Leina Sun
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jianwen Qin
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, China
| | - Yan Yin
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, China
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Xie B, Qiu Y, Zhou J, Du D, Ma H, Ji J, Zhu L, Zhang W. Establishment of an acquired lorlatinib-resistant cell line of non-small cell lung cancer and its mediated resistance mechanism. Clin Transl Oncol 2022; 24:2231-2240. [PMID: 35852680 DOI: 10.1007/s12094-022-02884-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022]
Abstract
PURPOSE Although lorlatinib, the third generation of echinoderm microtubule protein 4-anaplastic lymphoma kinase (EML4-ALK) tyrosine kinase inhibitor (TKI), overcame the previous generation ALK-TKIs' drug resistance problems, but the mechanism of lorlatinib resistance remained unclear. Furthermore, optimal chemotherapy for lorlatinib-resistant non-small cell lung cancer (NSCLC) patients was still unknown. METHODS A lorlatinib-resistant NSCLC cell line SNU-2535LR was generated by gradually increasing dose of lorlatinib to crizotinib-resistant cell line SNU-2535 in vitro. To study the resistance mechanism of SNU-2535LR cells, we applied CCK-8 assay to detect the sensitivity of crizotinib and the reverse effect of APR-246, a p53 activator, on lorlatinib-induced resistance and different chemotherapy drugs to SNU-2535LR cells. We also detected the expressions of EML4-ALK-related proteins of SNU-2535LR cells via western blot.Please confirm that author names have been identified correctly and are presented in the right order.Dear Editor: I have carefully confirmed that the author names have been identified correctly and are presented in right order.Thank you very much! Your sincerely BoXie RESULTS: The sensitivity of SNU-2535LR cells to lorlatinib was decreased significantly than that of SNU-2535 cells. EML4-ALK fusion was decreased both at protein level and DNA level in SNU-2535LR cells. More interesting, the crizotinib-resistant mutation ALK p.G1269A disappeared, while new TP53 mutation emerged in SNU-2535LR cells. APR-246 can reverse the lorlatinib resistance in SNU-2535LR cells, with a reversal index of 4.768. Compared with SNU-2535 cells, the sensitivity of SNU-2535LR cells to gemcitabine, docetaxel and paclitaxel was significantly increased (P < 0.05), but decreased to cisplatin (P < 0.05). CONCLUSION This study demonstrated that the combination of p53 protein agonist and lorlatinib may provide a new therapeutic strategy for NSCLC patients with lorlatinib resistance and TP53 mutation. Furthermore, the results also provide guidance for selecting optimal chemo-regimens for NSCLC patients after ALK-TKIs failure.
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Affiliation(s)
- Bo Xie
- Department of Oncology, General Hospital of Southern Theater Command, PLA, No.111, Liuhua Rd., Guangzhou, 510010, China
| | - Ying Qiu
- Department of Oncology, General Hospital of Southern Theater Command, PLA, No.111, Liuhua Rd., Guangzhou, 510010, China
| | - Juan Zhou
- Department of Oncology, General Hospital of Southern Theater Command, PLA, No.111, Liuhua Rd., Guangzhou, 510010, China
| | - Dou Du
- Department of Oncology, General Hospital of Southern Theater Command, PLA, No.111, Liuhua Rd., Guangzhou, 510010, China
| | - Haochuan Ma
- Department of Oncology, General Hospital of Southern Theater Command, PLA, No.111, Liuhua Rd., Guangzhou, 510010, China
| | - Jiapeng Ji
- Department of Oncology, General Hospital of Southern Theater Command, PLA, No.111, Liuhua Rd., Guangzhou, 510010, China
| | - Liquan Zhu
- Department of Oncology, General Hospital of Southern Theater Command, PLA, No.111, Liuhua Rd., Guangzhou, 510010, China
| | - Weimin Zhang
- Department of Oncology, General Hospital of Southern Theater Command, PLA, No.111, Liuhua Rd., Guangzhou, 510010, China.
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Baba K, Goto Y. Lorlatinib as a treatment for ALK-positive lung cancer. Future Oncol 2022; 18:2745-2766. [PMID: 35787143 DOI: 10.2217/fon-2022-0184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Lorlatinib, a third-generation ALK tyrosine kinase inhibitor, has been approved as a treatment for ALK-positive lung cancer. This review provides information regarding the pharmacology and clinical features of lorlatinib, including its efficacy and associated adverse events. Pivotal clinical trials are discussed along with the current status of lorlatinib as a treatment for ALK-positive lung cancer and future therapeutic challenges.
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Affiliation(s)
- Keisuke Baba
- Department of Thoracic Oncology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Yasushi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
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Liang S, Wang Q, Qi X, Liu Y, Li G, Lu S, Mou L, Chen X. Deciphering the Mechanism of Gilteritinib Overcoming Lorlatinib Resistance to the Double Mutant I1171N/F1174I in Anaplastic Lymphoma Kinase. Front Cell Dev Biol 2021; 9:808864. [PMID: 35004700 PMCID: PMC8733690 DOI: 10.3389/fcell.2021.808864] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/06/2021] [Indexed: 01/01/2023] Open
Abstract
Anaplastic lymphoma kinase (ALK) is validated as a therapeutic molecular target in multiple malignancies, such as non-small cell lung cancer (NSCLC). However, the feasibility of targeted therapies exerted by ALK inhibitors is inevitably hindered owing to drug resistance. The emergence of clinically acquired drug mutations has become a major challenge to targeted therapies and personalized medicines. Thus, elucidating the mechanism of resistance to ALK inhibitors is helpful for providing new therapeutic strategies for the design of next-generation drug. Here, we used molecular docking and multiple molecular dynamics simulations combined with correlated and energetical analyses to explore the mechanism of how gilteritinib overcomes lorlatinib resistance to the double mutant ALK I1171N/F1174I. We found that the conformational dynamics of the ALK kinase domain was reduced by the double mutations I1171N/F1174I. Moreover, energetical and structural analyses implied that the double mutations largely disturbed the conserved hydrogen bonding interactions from the hinge residues Glu1197 and Met1199 in the lorlatinib-bound state, whereas they had no discernible adverse impact on the binding affinity and stability of gilteritinib-bound state. These discrepancies created the capacity of the double mutant ALK I1171N/F1174I to confer drug resistance to lorlatinib. Our result anticipates to provide a mechanistic insight into the mechanism of drug resistance induced by ALK I1171N/F1174I that are resistant to lorlatinib treatment in NSCLC.
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Affiliation(s)
- Shuai Liang
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, China
| | - Qing Wang
- Oncology Department, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Xuesen Qi
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, China
| | - Yudi Liu
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, China
| | - Guozhen Li
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, China
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Linkai Mou
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, China
| | - Xiangyu Chen
- School of Medical Laboratory, Weifang Medical University, Weifang, China
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Pan Y, Deng C, Qiu Z, Cao C, Wu F. The Resistance Mechanisms and Treatment Strategies for ALK-Rearranged Non-Small Cell Lung Cancer. Front Oncol 2021; 11:713530. [PMID: 34660278 PMCID: PMC8517331 DOI: 10.3389/fonc.2021.713530] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/13/2021] [Indexed: 12/19/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a validated molecular target for non-small-cell lung cancer (NSCLC). The use of tyrosine kinase inhibitors (TKIs) has led to significantly improved survival benefits. However, the clinical benefits of targeting ALK using TKIs are limited due to the emergence of drug resistance. The landscape of resistance mechanisms and treatment decisions has become increasingly complex. Therefore, continued research into new drugs and combinatorial therapies is required to improve outcomes in NSCLC. In this review, we explore the resistance mechanisms of ALK TKIs in advanced NSCLC in order to provide a theoretical basis and research ideas for solving the problem of ALK drug resistance.
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Affiliation(s)
- Yue Pan
- Department of Oncology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Chao Deng
- Department of Oncology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Qiu
- Department of Oncology, Second Xiangya Hospital, Central South University, Changsha, China
| | | | - Fang Wu
- Department of Oncology, Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Cancer Mega-Data Intelligent Application and Engineering Research Centre, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, China
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Making NSCLC Crystal Clear: How Kinase Structures Revolutionized Lung Cancer Treatment. CRYSTALS 2020. [DOI: 10.3390/cryst10090725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The parallel advances of different scientific fields provide a contemporary scenario where collaboration is not a differential, but actually a requirement. In this context, crystallography has had a major contribution on the medical sciences, providing a “face” for targets of diseases that previously were known solely by name or sequence. Worldwide, cancer still leads the number of annual deaths, with 9.6 million associated deaths, with a major contribution from lung cancer and its 1.7 million deaths. Since the relationship between cancer and kinases was unraveled, these proteins have been extensively explored and became associated with drugs that later attained blockbuster status. Crystallographic structures of kinases related to lung cancer and their developed and marketed drugs provided insight on their conformation in the absence or presence of small molecules. Notwithstanding, these structures were also of service once the initially highly successful drugs started to lose their effectiveness in the emergence of mutations. This review focuses on a subclassification of lung cancer, non-small cell lung cancer (NSCLC), and major oncogenic driver mutations in kinases, and how crystallographic structures can be used, not only to provide awareness of the function and inhibition of these mutations, but also how these structures can be used in further computational studies aiming at addressing these novel mutations in the field of personalized medicine.
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Molecular Modeling of ALK L1198F and/or G1202R Mutations to Determine Differential Crizotinib Sensitivity. Sci Rep 2019; 9:11390. [PMID: 31388026 PMCID: PMC6684801 DOI: 10.1038/s41598-019-46825-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/17/2019] [Indexed: 01/29/2023] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that has been recognized as a therapeutic target for EML4-ALK fusion-positive nonsmall cell lung cancer (NSCLC) treatment using type I kinase inhibitors such as crizotinib to take over the ATP binding site. According to Shaw’s measurements, ALK carrying G1202R mutation shows reduced response to crizotinib (IC50 = 382 nM vs. IC50 = 20 nM for wild-type), whereas L1198F mutant is more responsive (IC50 = 0.4 nM). Interestingly, the double mutant L1198F/G1202R maintains a similar response (IC50 = 31 nM) to the wild-type. Herein we conducted molecular modeling simulations to elucidate the varied crizotinib sensitivities in three mutants carrying L1198F and/or G1202R. Both L1198 and G1202 are near the ATP pocket. Mutation G1202R causes steric hindrance that blocks crizotinib accessibility, which greatly reduces efficacy, whereas mutation L1198F enlarges the binding pocket entrance and hydrophobically interacts with crizotinib to enhance sensitivity. With respect to the double mutant L1198F/G1202R, F1198 indirectly pulls R1202 away from the binding entrance and consequently alleviates the steric obstacle introduced by R1202. These results demonstrated how the mutated residues tune the crizotinib response and may assist kinase inhibitor development especially for ALK G1202R, analogous to the ROS1 G2302R and MET G1163R mutations that are also resistant to crizotinib treatment in NSCLC.
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Morley JE, Vellas B. Patient-Centered (P4) Medicine and the Older Person. J Am Med Dir Assoc 2019; 18:455-459. [PMID: 28549701 DOI: 10.1016/j.jamda.2017.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/25/2022]
Affiliation(s)
- John E Morley
- Division of Geriatric Medicine, Saint Louis University School of Medicine, St. Louis, MO.
| | - Bruno Vellas
- Gérontopôle, CHU Toulouse University Hospital and INSERM U1027, Toulouse, France
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Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- 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
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Single-Molecule Imaging and Computational Microscopy Approaches Clarify the Mechanism of the Dimerization and Membrane Interactions of Green Fluorescent Protein. Int J Mol Sci 2019; 20:ijms20061410. [PMID: 30897814 PMCID: PMC6471090 DOI: 10.3390/ijms20061410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 02/01/2023] Open
Abstract
Green fluorescent protein (GFP) is widely used as a biomarker in living systems; however, GFP and its variants are prone to forming low-affinity dimers under physiological conditions. This undesirable tendency is exacerbated when fluorescent proteins (FP) are confined to membranes, fused to naturally-oligomeric proteins, or expressed at high levels in cells. Oligomerization of FPs introduces artifacts into the measurement of subunit stoichiometry, as well as interactions between proteins fused to FPs. Introduction of a single mutation, A206K, has been shown to disrupt hydrophobic interactions in the region responsible for GFP dimerization, thereby contributing to its monomerization. Nevertheless, a detailed understanding of how this single amino acid-dependent inhibition of dimerization in GFP occurs at the atomic level is still lacking. Single-molecule experiments combined with computational microscopy (atomistic molecular dynamics) revealed that the amino group of A206 contributes to GFP dimer formation via a multivalent electrostatic interaction. We further showed that myristoyl modification is an efficient mechanism to promote membrane attachment of GFP. Molecular dynamics-based site-directed mutagenesis has been used to identify the key functional residues in FPs. The data presented here have been utilized as a monomeric control in downstream single-molecule studies, facilitating more accurate stoichiometry quantification of functional protein complexes in living cells.
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Okada K, Araki M, Sakashita T, Ma B, Kanada R, Yanagitani N, Horiike A, Koike S, Oh-Hara T, Watanabe K, Tamai K, Maemondo M, Nishio M, Ishikawa T, Okuno Y, Fujita N, Katayama R. Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance. EBioMedicine 2019; 41:105-119. [PMID: 30662002 PMCID: PMC6441848 DOI: 10.1016/j.ebiom.2019.01.019] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Alectinib has shown a greater efficacy to ALK-rearranged non-small-cell lung cancers in first-line setting; however, most patients relapse due to acquired resistance, such as secondary mutations in ALK including I1171N and G1202R. Although ceritinib or lorlatinib was shown to be effective to these resistant mutants, further resistance often emerges due to ALK-compound mutations in relapse patients following the use of ceritinib or lorlatinib. However, the drug for overcoming resistance has not been established yet. METHODS We established lorlatinib-resistant cells harboring ALK-I1171N or -G1202R compound mutations by performing ENU mutagenesis screening or using an in vivo mouse model. We performed drug screening to overcome the lorlatinib-resistant ALK-compound mutations. To evaluate these resistances in silico, we developed a modified computational molecular dynamic simulation (MP-CAFEE). FINDINGS We identified 14 lorlatinib-resistant ALK-compound mutants, including several mutants that were recently discovered in lorlatinib-resistant patients. Some of these compound mutants were found to be sensitive to early generation ALK-TKIs and several BCR-ABL inhibitors. Using our original computational simulation, we succeeded in demonstrating a clear linear correlation between binding free energy and in vitro experimental IC50 value of several ALK-TKIs to single- or compound-mutated EML4-ALK expressing Ba/F3 cells and in recapitulating the tendency of the binding affinity reduction by double mutations found in this study. Computational simulation revealed that ALK-L1256F single mutant conferred resistance to lorlatinib but increased the sensitivity to alectinib. INTERPRETATION We discovered lorlatinib-resistant multiple ALK-compound mutations and an L1256F single mutation as well as the potential therapeutic strategies for these ALK mutations. Our original computational simulation to calculate the binding affinity may be applicable for predicting resistant mutations and for overcoming drug resistance in silico. FUND: This work was mainly supported by MEXT/JSPS KAKENHI Grants and AMED Grants.
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Affiliation(s)
- Koutaroh Okada
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Mitsugu Araki
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takuya Sakashita
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Biao Ma
- Research and Development Group for In Silico Drug Discovery, Pro-Cluster Kobe, Foundation for Biomedical Research and Innovation (FBRI), 6-3-5, Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Ryo Kanada
- RIKEN Compass to Healthy Life Research Complex Program, 6-3-5, Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Noriko Yanagitani
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Atsushi Horiike
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sumie Koike
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tomoko Oh-Hara
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kana Watanabe
- Department of Respiratory Medicine, Miyagi Cancer Center, Miyagi, Japan
| | - Keiichi Tamai
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Miyagi, Japan
| | - Makoto Maemondo
- Department of Respiratory Medicine, Miyagi Cancer Center, Miyagi, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Yasushi Okuno
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naoya Fujita
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
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Fan S, Wang R, Li C, Bai L, Zhao YL, Shi T. Insight into Structural Characteristics of Protein-Substrate Interaction in Pimaricin Thioesterase. Int J Mol Sci 2019; 20:ijms20040877. [PMID: 30781619 PMCID: PMC6412417 DOI: 10.3390/ijms20040877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 01/23/2023] Open
Abstract
As a polyene antibiotic of great pharmaceutical significance, pimaricin has been extensively studied to enhance its productivity and effectiveness. In our previous studies, pre-reaction state (PRS) has been validated as one of the significant conformational categories before macrocyclization, and is critical to mutual recognition and catalytic preparation in thioesterase (TE)-catalyzed systems. In our study, molecular dynamics (MD) simulations were conducted on pimaricin TE-polyketide complex and PRS, as well as pre-organization state (POS), a molecular conformation possessing a pivotal intra-molecular hydrogen bond, were detected. Conformational transition between POS and PRS was observed in one of the simulations, and POS was calculated to be energetically more stable than PRS by 4.58 kcal/mol. The structural characteristics of PRS and POS-based hydrogen-bonding, and hydrophobic interactions were uncovered, and additional simulations were carried out to rationalize the functions of several key residues (Q29, M210, and R186). Binding energies, obtained from MM/PBSA calculations, were further decomposed to residues, in order to reveal their roles in product release. Our study advanced a comprehensive understanding of pimaricin TE-catalyzed macrocyclization from the perspectives of conformational change, protein-polyketide recognition, and product release, and provided potential residues for rational modification of pimaricin TE.
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Affiliation(s)
- Shuobing Fan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Rufan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Chen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Wang H, Wang Y, Guo W, Du B, Huang X, Wu R, Yang B, Lin X, Wu Y. Insight into resistance mechanism of anaplastic lymphoma kinase to alectinib and JH-VIII-157-02 caused by G1202R solvent front mutation. Drug Des Devel Ther 2018; 12:1183-1193. [PMID: 29785088 PMCID: PMC5953303 DOI: 10.2147/dddt.s147104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Mutated anaplastic lymphoma kinase (ALK) drives the development of advanced non-small cell lung cancer (NSCLC). Most reported small-molecule inhibitors targeting the ALK domain do not display good inhibition of the G1202R solvent front mutation. The solvent front mutation was assumed to hinder drug binding. However, a different fact could be uncovered by the simulations reported in this study through a structural analog of alectinib (JH-VIII-157-02), which demonstrated potent effects against the G1202R mutation. METHODS Molecular docking, conventional molecular dynamics (MD) simulations, free energy calculations, and umbrella sampling (US) simulations were carried out to make clear the principles of the binding preferences of alectinib and JH-VIII-157-02 toward ALKWT and the ALK G1202R (ALKG1202R) mutation. RESULTS JH-VIII-157-02 has similar binding affinities to both ALKWT and ALKG1202R whereas it has has a much lower binding affinity for alectinib to ALKG1202R. Analysis of individual energy terms indicate the major variation involves the van der Waals and entropy terms. Structural analysis reveals that the conformational change of the ATP-binding glycine-rich loop was primarily responsible for the alectinib resistance, not JH-VIII-157-02. In addition, US simulations prove JH-VIII-157-02 has similar dissociative processes from both ALKWT and ALKG1202R, while alectinib is more easily dissociated from ALKG1202R than from ALKWT, thus indicating lesser residence time. CONCLUSION Both the binding affinity and the drug residence time should be emphasized in rational drug design to overcome the G1202R solvent front mutation in ALK resistance.
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Affiliation(s)
- Han Wang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, People’s Republic of China
- Stem Cell Research Institute, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, People’s Republic of China
| | - Yao Wang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, People’s Republic of China
- Stem Cell Research Institute, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, People’s Republic of China
| | - Wentao Guo
- School of Pharmacy, Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Bin Du
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, People’s Republic of China
- Stem Cell Research Institute, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, People’s Republic of China
| | - Xiaobing Huang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, People’s Republic of China
- Stem Cell Research Institute, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, People’s Republic of China
| | - Riping Wu
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, People’s Republic of China
- Stem Cell Research Institute, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, People’s Republic of China
| | - Baoyu Yang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, People’s Republic of China
- Stem Cell Research Institute, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, People’s Republic of China
| | - Xiaoyan Lin
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, People’s Republic of China
- Stem Cell Research Institute, Fujian Medical University, Fuzhou, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, People’s Republic of China
- Graduate School of Education, Fujian Medical University, Fuzhou, People’s Republic of China
| | - Yilan Wu
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, People’s Republic of China
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Chen C, He Z, Xie D, Zheng L, Zhao T, Zhang X, Cheng D. Molecular Mechanism Behind the Resistance of the G1202R-Mutated Anaplastic Lymphoma Kinase to the Approved Drug Ceritinib. J Phys Chem B 2018; 122:4680-4692. [PMID: 29648831 DOI: 10.1021/acs.jpcb.8b02040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Anaplastic lymphoma kinase (ALK) has been regarded as an essential target for the treatment of nonsmall cell lung cancer (NSCLC). However, the emergence of the G1202R solvent front mutation that confers resistance to the drugs was reported for the first as well as the second generation ALK inhibitors. It was thought that the G1202R solvent front mutation might hinder the drug binding. In this study, a different fact could be clarified by multiple molecular modeling methodologies through a structural analogue of ceritinib (compound 10, Cpd-10) that is reported to be a potent inhibitor against the G1202R mutation. Herein, molecular docking, accelerated molecular dynamics (aMD) simulations in conjunction with principal component analysis (PCA), and free energy map calculations were used to produce reasonable and representative initial conformations for the conventional MD simulations. Compared with Cpd-10, the binding specificity of ceritinib between ALK wild-type (ALKWT) and ALK G1202R (ALKG1202R) are primarily controlled by the conformational change of the P-loop- and A-loop-induced energetic redistributions, and the variation is nonpolar interactions, as indicated by conventional MD simulations, PCA, dynamic cross-correlation map (DCCM) analysis, and free energy calculations. Furthermore, the umbrella sampling (US) simulations were carried out to make clear the principle of the dissociation processes of ceritinib and Cpd-10 toward ALKWT and ALKG1202R. The calculation results suggest that Cpd-10 has similar dissociation processes from both ALKWT and ALKG1202R, but ceritinib is more easily dissociated from ALKG1202R than from ALKWT, thus less residence time is responsible for the ceritinib resistance. Our results suggest that both the binding specificity and the drug residence time should be emphasized in rational drug design to overcome the G1202R solvent front mutation of ALK resistance.
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Affiliation(s)
- Chaohong Chen
- Department of Thoracic Cardiovascular , The First Affiliated Hospital of Wenzhou Medical University , Wenzhou 325000 , China
| | - Zhifeng He
- Department of Thoracic Cardiovascular , The First Affiliated Hospital of Wenzhou Medical University , Wenzhou 325000 , China
| | - Deyao Xie
- Department of Thoracic Cardiovascular , The First Affiliated Hospital of Wenzhou Medical University , Wenzhou 325000 , China
| | - Liangcheng Zheng
- Department of Thoracic Cardiovascular , The First Affiliated Hospital of Wenzhou Medical University , Wenzhou 325000 , China
| | - Tianhao Zhao
- Department of Thoracic Cardiovascular , The First Affiliated Hospital of Wenzhou Medical University , Wenzhou 325000 , China
| | - Xinbo Zhang
- Department of Thoracic Cardiovascular , The First Affiliated Hospital of Wenzhou Medical University , Wenzhou 325000 , China
| | - Dezhi Cheng
- Department of Thoracic Cardiovascular , The First Affiliated Hospital of Wenzhou Medical University , Wenzhou 325000 , China
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Liu Z, Bao Y, Li B, Sun X, Wang L. Does ALK-rearrangement predict favorable response to the therapy of bevacizumab plus pemetrexed in advanced non-small-cell lung cancer? Case report and literature review. Clin Transl Med 2018; 7:1. [PMID: 29318404 PMCID: PMC5760484 DOI: 10.1186/s40169-017-0178-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022] Open
Abstract
Background Advanced ALK-rearranged non-small cell lung cancer (NSCLC) patients will develop acquired resistance after anaplastic lymphoma kinase (ALK) inhibitors therapies. Vascular endothelial growth factor-A (VEGF-A) production and tumor vessel formation were found to be more significantly enriched in ALK-rearrangement NSCLC than that in epidermal growth factor receptor or Kirsten rat sarcoma viral oncogene mutated NSCLC. However, the correlation between ALK rearrangement and the efficacy of bevacizumab (a recombinant humanized IgG1 monoclonal antibody targeting VEGF-A) was still elusive. Case presentation We report a case with metastatic NSCLC harboring ALK-rearrangement who was initially resistant to two courses of ALK-Tyrosine Kinase Inhibitor (TKI) therapy, but got a clinical benefit of 7 months of progression free survival after the combined treatment of bevacizumab plus pemetrexed. And the patient tolerated well. Conclusions It suggested that bevacizumab combined with pemetrexed might be a preferred option for ALK rearrangement patient who had failed no less than two courses of ALK-TKIs.
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Affiliation(s)
- Zhichao Liu
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, 250200, China.,Department of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Science, No. 440, Ji Yan Road, Jinan, 250017, Shandong, China
| | - Youting Bao
- Department of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Science, No. 440, Ji Yan Road, Jinan, 250017, Shandong, China.,Clinical College, Weifang Medical University, Weifang, 261053, China
| | - Butuo Li
- Department of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Science, No. 440, Ji Yan Road, Jinan, 250017, Shandong, China
| | - Xindong Sun
- Department of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Science, No. 440, Ji Yan Road, Jinan, 250017, Shandong, China
| | - Linlin Wang
- Department of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Science, No. 440, Ji Yan Road, Jinan, 250017, Shandong, China.
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Inamura K. Renal Cell Tumors: Understanding Their Molecular Pathological Epidemiology and the 2016 WHO Classification. Int J Mol Sci 2017; 18:E2195. [PMID: 29053609 PMCID: PMC5666876 DOI: 10.3390/ijms18102195] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence suggests that renal cell tumors represent a group of histologically and molecularly heterogeneous diseases, even within the same histological subtype. In accordance with the increased understanding of the morphological, immunohistochemical, molecular, and epidemiological characteristics of renal cell tumors, the World Health Organization (WHO) classification of renal cell tumors has been modified. This review provides perspectives on both new and current subtypes of renal cell tumors, as well as on the emerging/provisional renal cell carcinomas in the new 2016 WHO classification, which focuses on features of their molecular pathological epidemiology. The WHO classification will require additional revisions to enable the classification of renal cell tumors as clinically meaningful subtypes and provide a better understanding of the unique characteristics of renal cell tumors.
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Affiliation(s)
- Kentaro Inamura
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
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Inamura K. Translocation Renal Cell Carcinoma: An Update on Clinicopathological and Molecular Features. Cancers (Basel) 2017; 9:cancers9090111. [PMID: 28850056 PMCID: PMC5615326 DOI: 10.3390/cancers9090111] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/24/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022] Open
Abstract
Microphthalmia-associated transcription (MiT) family translocation renal cell carcinoma (tRCC) comprises Xp11 tRCC and t(6;11) RCC. Due to the presence of fusion genes, Xp11 tRCC and t(6;11) RCC are also known as TFE3- and TFEB-rearranged RCC, respectively. TFE3 and TFEB belong to the MiT family, which regulates melanocyte and osteoclast differentiation, and TFE3- and TFEB-rearranged RCC show characteristic clinicopathological and immunohistochemical features. Recent studies identified the fusion partner-dependent clinicopathological and immunohistochemical features in TFE3-rearranged RCC. Furthermore, RCC with chromosome 6p amplification, including TFEB, was identified as a unique subtype of RCC, along with ALK-rearranged RCC. This review summarizes these recent advancements in our tRCC-related knowledge.
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Affiliation(s)
- Kentaro Inamura
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
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